Load Data

dataset <- read.delim("raw_data/Figure5A.txt", stringsAsFactors = FALSE)

dataset$genotype <- gsub(" ", "", dataset$genotype )
dataset$genotype <- factor(dataset$genotype)
dataset$Experiment <- factor(rep(paste0("exp", 1:(length(dataset$genotype)/length(levels(dataset$genotype)))), each=length(unique(dataset$genotype))))

dataset$siRNA <-  factor(gsub(".*[T,O]\\+","",dataset$genotype))
dataset$genotype <-  factor(gsub("\\+.*","",dataset$genotype))

dataset$UID <- factor(paste(dataset$Experiment, dataset$genotype, dataset$siRNA))
dataset$GSID <- factor(paste(dataset$genotype, dataset$siRNA))

# wide format
kable(dataset, row.names = F)
genotype NT olaparib_30nM olaparib_300nM olaparib_3000nM Experiment siRNA UID GSID
WT 2668 2328 2108 1012 exp1 siCtrl exp1 WT siCtrl WT siCtrl
WT 2336 1888 1336 796 exp1 si53BP1 exp1 WT si53BP1 WT si53BP1
WT 1080 804 486 246 exp1 siBRCA1 exp1 WT siBRCA1 WT siBRCA1
WT 1360 992 840 468 exp1 si53BP1+siBRCA1 exp1 WT si53BP1+siBRCA1 WT si53BP1+siBRCA1
ALC1KO 1960 1040 576 378 exp1 siCtrl exp1 ALC1KO siCtrl ALC1KO siCtrl
ALC1KO 1672 792 536 388 exp1 si53BP1 exp1 ALC1KO si53BP1 ALC1KO si53BP1
ALC1KO 752 324 164 71 exp1 siBRCA1 exp1 ALC1KO siBRCA1 ALC1KO siBRCA1
ALC1KO 788 478 293 142 exp1 si53BP1+siBRCA1 exp1 ALC1KO si53BP1+siBRCA1 ALC1KO si53BP1+siBRCA1
WT 3072 2864 2768 2084 exp2 siCtrl exp2 WT siCtrl WT siCtrl
WT 3208 2984 2500 1886 exp2 si53BP1 exp2 WT si53BP1 WT si53BP1
WT 2376 1352 1112 1020 exp2 siBRCA1 exp2 WT siBRCA1 WT siBRCA1
WT 2744 2592 2016 1832 exp2 si53BP1+siBRCA1 exp2 WT si53BP1+siBRCA1 WT si53BP1+siBRCA1
ALC1KO 2064 1032 488 411 exp2 siCtrl exp2 ALC1KO siCtrl ALC1KO siCtrl
ALC1KO 1424 988 536 416 exp2 si53BP1 exp2 ALC1KO si53BP1 ALC1KO si53BP1
ALC1KO 372 195 94 68 exp2 siBRCA1 exp2 ALC1KO siBRCA1 ALC1KO siBRCA1
ALC1KO 612 153 64 45 exp2 si53BP1+siBRCA1 exp2 ALC1KO si53BP1+siBRCA1 ALC1KO si53BP1+siBRCA1
WT 2744 2728 2464 1838 exp3 siCtrl exp3 WT siCtrl WT siCtrl
WT 2800 2608 2320 1748 exp3 si53BP1 exp3 WT si53BP1 WT si53BP1
WT 1848 1256 1020 768 exp3 siBRCA1 exp3 WT siBRCA1 WT siBRCA1
WT 2328 2624 2104 2064 exp3 si53BP1+siBRCA1 exp3 WT si53BP1+siBRCA1 WT si53BP1+siBRCA1
ALC1KO 2048 988 812 540 exp3 siCtrl exp3 ALC1KO siCtrl ALC1KO siCtrl
ALC1KO 1624 1096 528 304 exp3 si53BP1 exp3 ALC1KO si53BP1 ALC1KO si53BP1
ALC1KO 380 376 126 47 exp3 siBRCA1 exp3 ALC1KO siBRCA1 ALC1KO siBRCA1
ALC1KO 896 288 168 75 exp3 si53BP1+siBRCA1 exp3 ALC1KO si53BP1+siBRCA1 ALC1KO si53BP1+siBRCA1
WT 1576 1496 1328 948 exp4 siCtrl exp4 WT siCtrl WT siCtrl
WT 2088 1960 1856 1076 exp4 si53BP1 exp4 WT si53BP1 WT si53BP1
WT 608 512 376 191 exp4 siBRCA1 exp4 WT siBRCA1 WT siBRCA1
WT 1352 960 796 876 exp4 si53BP1+siBRCA1 exp4 WT si53BP1+siBRCA1 WT si53BP1+siBRCA1
ALC1KO 1304 436 396 85 exp4 siCtrl exp4 ALC1KO siCtrl ALC1KO siCtrl
ALC1KO 370 184 111 38 exp4 si53BP1 exp4 ALC1KO si53BP1 ALC1KO si53BP1
ALC1KO 580 224 108 11 exp4 siBRCA1 exp4 ALC1KO siBRCA1 ALC1KO siBRCA1
ALC1KO 1416 712 500 312 exp4 si53BP1+siBRCA1 exp4 ALC1KO si53BP1+siBRCA1 ALC1KO si53BP1+siBRCA1
library(reshape2)
# reshape to long format
dataset <- melt(dataset, variable.name = "Treatment", value.name = "Counts")

dataset$genotype <- relevel(dataset$genotype, ref = "WT")
dataset$siRNA <- relevel(dataset$siRNA, ref = "siCtrl")
dataset$UID <- relevel(dataset$UID, ref = "exp1 WT siCtrl")

dataset$Olaparib <- gsub("NT","1",dataset$Treatment)
dataset$Olaparib <- gsub("olaparib_|nM","",dataset$Olaparib)
dataset$Olaparib <- log10(as.integer(dataset$Olaparib))




dataset$Offset <- NA
for(uid in levels(dataset$UID)){
        dataset$Offset[dataset$UID == uid] <- mean(dataset$Counts[dataset$UID == uid])
}

dataset$NormCounts <- dataset$Counts / dataset$Offset



dataset$Offset2 <- NA
for(gsid in levels(dataset$GSID)){
        dataset$Offset2[dataset$GSID == gsid] <- mean(dataset$NormCounts[dataset$GSID == gsid & dataset$Olaparib == 0])
}

dataset$NormCounts2 <- dataset$NormCounts / dataset$Offset2



# long format
kable(dataset, row.names = F)
genotype Experiment siRNA UID GSID Treatment Counts Olaparib Offset NormCounts Offset2 NormCounts2
WT exp1 siCtrl exp1 WT siCtrl WT siCtrl NT 2668 0.000000 2029.00 1.3149335 1.188929 1.1059818
WT exp1 si53BP1 exp1 WT si53BP1 WT si53BP1 NT 2336 0.000000 1589.00 1.4701070 1.265421 1.1617529
WT exp1 siBRCA1 exp1 WT siBRCA1 WT siBRCA1 NT 1080 0.000000 654.00 1.6513761 1.556467 1.0609770
WT exp1 si53BP1+siBRCA1 exp1 WT si53BP1+siBRCA1 WT si53BP1+siBRCA1 NT 1360 0.000000 915.00 1.4863388 1.264986 1.1749846
ALC1KO exp1 siCtrl exp1 ALC1KO siCtrl ALC1KO siCtrl NT 1960 0.000000 988.50 1.9828022 2.066197 0.9596386
ALC1KO exp1 si53BP1 exp1 ALC1KO si53BP1 ALC1KO si53BP1 NT 1672 0.000000 847.00 1.9740260 1.900335 1.0387778
ALC1KO exp1 siBRCA1 exp1 ALC1KO siBRCA1 ALC1KO siBRCA1 NT 752 0.000000 327.75 2.2944317 2.121324 1.0816038
ALC1KO exp1 si53BP1+siBRCA1 exp1 ALC1KO si53BP1+siBRCA1 ALC1KO si53BP1+siBRCA1 NT 788 0.000000 425.25 1.8530276 2.273009 0.8152311
WT exp2 siCtrl exp2 WT siCtrl WT siCtrl NT 3072 0.000000 2697.00 1.1390434 1.188929 0.9580418
WT exp2 si53BP1 exp2 WT si53BP1 WT si53BP1 NT 3208 0.000000 2644.50 1.2130838 1.265421 0.9586401
WT exp2 siBRCA1 exp2 WT siBRCA1 WT siBRCA1 NT 2376 0.000000 1465.00 1.6218430 1.556467 1.0420025
WT exp2 si53BP1+siBRCA1 exp2 WT si53BP1+siBRCA1 WT si53BP1+siBRCA1 NT 2744 0.000000 2296.00 1.1951220 1.264986 0.9447711
ALC1KO exp2 siCtrl exp2 ALC1KO siCtrl ALC1KO siCtrl NT 2064 0.000000 998.75 2.0665832 2.066197 1.0001871
ALC1KO exp2 si53BP1 exp2 ALC1KO si53BP1 ALC1KO si53BP1 NT 1424 0.000000 841.00 1.6932224 1.900335 0.8910125
ALC1KO exp2 siBRCA1 exp2 ALC1KO siBRCA1 ALC1KO siBRCA1 NT 372 0.000000 182.25 2.0411523 2.121324 0.9622069
ALC1KO exp2 si53BP1+siBRCA1 exp2 ALC1KO si53BP1+siBRCA1 ALC1KO si53BP1+siBRCA1 NT 612 0.000000 218.50 2.8009153 2.273009 1.2322500
WT exp3 siCtrl exp3 WT siCtrl WT siCtrl NT 2744 0.000000 2443.50 1.1229793 1.188929 0.9445305
WT exp3 si53BP1 exp3 WT si53BP1 WT si53BP1 NT 2800 0.000000 2369.00 1.1819333 1.265421 0.9340235
WT exp3 siBRCA1 exp3 WT siBRCA1 WT siBRCA1 NT 1848 0.000000 1223.00 1.5110384 1.556467 0.9708127
WT exp3 si53BP1+siBRCA1 exp3 WT si53BP1+siBRCA1 WT si53BP1+siBRCA1 NT 2328 0.000000 2280.00 1.0210526 1.264986 0.8071653
ALC1KO exp3 siCtrl exp3 ALC1KO siCtrl ALC1KO siCtrl NT 2048 0.000000 1097.00 1.8669098 2.066197 0.9035489
ALC1KO exp3 si53BP1 exp3 ALC1KO si53BP1 ALC1KO si53BP1 NT 1624 0.000000 888.00 1.8288288 1.900335 0.9623718
ALC1KO exp3 siBRCA1 exp3 ALC1KO siBRCA1 ALC1KO siBRCA1 NT 380 0.000000 232.25 1.6361679 2.121324 0.7712957
ALC1KO exp3 si53BP1+siBRCA1 exp3 ALC1KO si53BP1+siBRCA1 ALC1KO si53BP1+siBRCA1 NT 896 0.000000 356.75 2.5115627 2.273009 1.1049506
WT exp4 siCtrl exp4 WT siCtrl WT siCtrl NT 1576 0.000000 1337.00 1.1787584 1.188929 0.9914459
WT exp4 si53BP1 exp4 WT si53BP1 WT si53BP1 NT 2088 0.000000 1745.00 1.1965616 1.265421 0.9455835
WT exp4 siBRCA1 exp4 WT siBRCA1 WT siBRCA1 NT 608 0.000000 421.75 1.4416123 1.556467 0.9262078
WT exp4 si53BP1+siBRCA1 exp4 WT si53BP1+siBRCA1 WT si53BP1+siBRCA1 NT 1352 0.000000 996.00 1.3574297 1.264986 1.0730790
ALC1KO exp4 siCtrl exp4 ALC1KO siCtrl ALC1KO siCtrl NT 1304 0.000000 555.25 2.3484917 2.066197 1.1366254
ALC1KO exp4 si53BP1 exp4 ALC1KO si53BP1 ALC1KO si53BP1 NT 370 0.000000 175.75 2.1052632 1.900335 1.1078379
ALC1KO exp4 siBRCA1 exp4 ALC1KO siBRCA1 ALC1KO siBRCA1 NT 580 0.000000 230.75 2.5135428 2.121324 1.1848936
ALC1KO exp4 si53BP1+siBRCA1 exp4 ALC1KO si53BP1+siBRCA1 ALC1KO si53BP1+siBRCA1 NT 1416 0.000000 735.00 1.9265306 2.273009 0.8475684
WT exp1 siCtrl exp1 WT siCtrl WT siCtrl olaparib_30nM 2328 1.477121 2029.00 1.1473632 1.188929 0.9650396
WT exp1 si53BP1 exp1 WT si53BP1 WT si53BP1 olaparib_30nM 1888 1.477121 1589.00 1.1881687 1.265421 0.9389510
WT exp1 siBRCA1 exp1 WT siBRCA1 WT siBRCA1 olaparib_30nM 804 1.477121 654.00 1.2293578 1.556467 0.7898384
WT exp1 si53BP1+siBRCA1 exp1 WT si53BP1+siBRCA1 WT si53BP1+siBRCA1 olaparib_30nM 992 1.477121 915.00 1.0841530 1.264986 0.8570476
ALC1KO exp1 siCtrl exp1 ALC1KO siCtrl ALC1KO siCtrl olaparib_30nM 1040 1.477121 988.50 1.0520991 2.066197 0.5091960
ALC1KO exp1 si53BP1 exp1 ALC1KO si53BP1 ALC1KO si53BP1 olaparib_30nM 792 1.477121 847.00 0.9350649 1.900335 0.4920527
ALC1KO exp1 siBRCA1 exp1 ALC1KO siBRCA1 ALC1KO siBRCA1 olaparib_30nM 324 1.477121 327.75 0.9885584 2.121324 0.4660101
ALC1KO exp1 si53BP1+siBRCA1 exp1 ALC1KO si53BP1+siBRCA1 ALC1KO si53BP1+siBRCA1 olaparib_30nM 478 1.477121 425.25 1.1240447 2.273009 0.4945183
WT exp2 siCtrl exp2 WT siCtrl WT siCtrl olaparib_30nM 2864 1.477121 2697.00 1.0619207 1.188929 0.8931744
WT exp2 si53BP1 exp2 WT si53BP1 WT si53BP1 olaparib_30nM 2984 1.477121 2644.50 1.1283797 1.265421 0.8917027
WT exp2 siBRCA1 exp2 WT siBRCA1 WT siBRCA1 olaparib_30nM 1352 1.477121 1465.00 0.9228669 1.556467 0.5929240
WT exp2 si53BP1+siBRCA1 exp2 WT si53BP1+siBRCA1 WT si53BP1+siBRCA1 olaparib_30nM 2592 1.477121 2296.00 1.1289199 1.264986 0.8924368
ALC1KO exp2 siCtrl exp2 ALC1KO siCtrl ALC1KO siCtrl olaparib_30nM 1032 1.477121 998.75 1.0332916 2.066197 0.5000935
ALC1KO exp2 si53BP1 exp2 ALC1KO si53BP1 ALC1KO si53BP1 olaparib_30nM 988 1.477121 841.00 1.1747919 1.900335 0.6182025
ALC1KO exp2 siBRCA1 exp2 ALC1KO siBRCA1 ALC1KO siBRCA1 olaparib_30nM 195 1.477121 182.25 1.0699588 2.121324 0.5043826
ALC1KO exp2 si53BP1+siBRCA1 exp2 ALC1KO si53BP1+siBRCA1 ALC1KO si53BP1+siBRCA1 olaparib_30nM 153 1.477121 218.50 0.7002288 2.273009 0.3080625
WT exp3 siCtrl exp3 WT siCtrl WT siCtrl olaparib_30nM 2728 1.477121 2443.50 1.1164313 1.188929 0.9390230
WT exp3 si53BP1 exp3 WT si53BP1 WT si53BP1 olaparib_30nM 2608 1.477121 2369.00 1.1008864 1.265421 0.8699762
WT exp3 siBRCA1 exp3 WT siBRCA1 WT siBRCA1 olaparib_30nM 1256 1.477121 1223.00 1.0269828 1.556467 0.6598164
WT exp3 si53BP1+siBRCA1 exp3 WT si53BP1+siBRCA1 WT si53BP1+siBRCA1 olaparib_30nM 2624 1.477121 2280.00 1.1508772 1.264986 0.9097946
ALC1KO exp3 siCtrl exp3 ALC1KO siCtrl ALC1KO siCtrl olaparib_30nM 988 1.477121 1097.00 0.9006381 2.066197 0.4358917
ALC1KO exp3 si53BP1 exp3 ALC1KO si53BP1 ALC1KO si53BP1 olaparib_30nM 1096 1.477121 888.00 1.2342342 1.900335 0.6494824
ALC1KO exp3 siBRCA1 exp3 ALC1KO siBRCA1 ALC1KO siBRCA1 olaparib_30nM 376 1.477121 232.25 1.6189451 2.121324 0.7631768
ALC1KO exp3 si53BP1+siBRCA1 exp3 ALC1KO si53BP1+siBRCA1 ALC1KO si53BP1+siBRCA1 olaparib_30nM 288 1.477121 356.75 0.8072880 2.273009 0.3551627
WT exp4 siCtrl exp4 WT siCtrl WT siCtrl olaparib_30nM 1496 1.477121 1337.00 1.1189230 1.188929 0.9411187
WT exp4 si53BP1 exp4 WT si53BP1 WT si53BP1 olaparib_30nM 1960 1.477121 1745.00 1.1232092 1.265421 0.8876167
WT exp4 siBRCA1 exp4 WT siBRCA1 WT siBRCA1 olaparib_30nM 512 1.477121 421.75 1.2139893 1.556467 0.7799645
WT exp4 si53BP1+siBRCA1 exp4 WT si53BP1+siBRCA1 WT si53BP1+siBRCA1 olaparib_30nM 960 1.477121 996.00 0.9638554 1.264986 0.7619496
ALC1KO exp4 siCtrl exp4 ALC1KO siCtrl ALC1KO siCtrl olaparib_30nM 436 1.477121 555.25 0.7852319 2.066197 0.3800373
ALC1KO exp4 si53BP1 exp4 ALC1KO si53BP1 ALC1KO si53BP1 olaparib_30nM 184 1.477121 175.75 1.0469417 1.900335 0.5509248
ALC1KO exp4 siBRCA1 exp4 ALC1KO siBRCA1 ALC1KO siBRCA1 olaparib_30nM 224 1.477121 230.75 0.9707476 2.121324 0.4576141
ALC1KO exp4 si53BP1+siBRCA1 exp4 ALC1KO si53BP1+siBRCA1 ALC1KO si53BP1+siBRCA1 olaparib_30nM 712 1.477121 735.00 0.9687075 2.273009 0.4261784
WT exp1 siCtrl exp1 WT siCtrl WT siCtrl olaparib_300nM 2108 2.477121 2029.00 1.0389354 1.188929 0.8738417
WT exp1 si53BP1 exp1 WT si53BP1 WT si53BP1 olaparib_300nM 1336 2.477121 1589.00 0.8407804 1.265421 0.6644272
WT exp1 siBRCA1 exp1 WT siBRCA1 WT siBRCA1 olaparib_300nM 486 2.477121 654.00 0.7431193 1.556467 0.4774396
WT exp1 si53BP1+siBRCA1 exp1 WT si53BP1+siBRCA1 WT si53BP1+siBRCA1 olaparib_300nM 840 2.477121 915.00 0.9180328 1.264986 0.7257258
ALC1KO exp1 siCtrl exp1 ALC1KO siCtrl ALC1KO siCtrl olaparib_300nM 576 2.477121 988.50 0.5827011 2.066197 0.2820163
ALC1KO exp1 si53BP1 exp1 ALC1KO si53BP1 ALC1KO si53BP1 olaparib_300nM 536 2.477121 847.00 0.6328217 1.900335 0.3330053
ALC1KO exp1 siBRCA1 exp1 ALC1KO siBRCA1 ALC1KO siBRCA1 olaparib_300nM 164 2.477121 327.75 0.5003814 2.121324 0.2358817
ALC1KO exp1 si53BP1+siBRCA1 exp1 ALC1KO si53BP1+siBRCA1 ALC1KO si53BP1+siBRCA1 olaparib_300nM 293 2.477121 425.25 0.6890065 2.273009 0.3031253
WT exp2 siCtrl exp2 WT siCtrl WT siCtrl olaparib_300nM 2768 2.477121 2697.00 1.0263255 1.188929 0.8632356
WT exp2 si53BP1 exp2 WT si53BP1 WT si53BP1 olaparib_300nM 2500 2.477121 2644.50 0.9453583 1.265421 0.7470699
WT exp2 siBRCA1 exp2 WT siBRCA1 WT siBRCA1 olaparib_300nM 1112 2.477121 1465.00 0.7590444 1.556467 0.4876712
WT exp2 si53BP1+siBRCA1 exp2 WT si53BP1+siBRCA1 WT si53BP1+siBRCA1 olaparib_300nM 2016 2.477121 2296.00 0.8780488 1.264986 0.6941175
ALC1KO exp2 siCtrl exp2 ALC1KO siCtrl ALC1KO siCtrl olaparib_300nM 488 2.477121 998.75 0.4886108 2.066197 0.2364783
ALC1KO exp2 si53BP1 exp2 ALC1KO si53BP1 ALC1KO si53BP1 olaparib_300nM 536 2.477121 841.00 0.6373365 1.900335 0.3353811
ALC1KO exp2 siBRCA1 exp2 ALC1KO siBRCA1 ALC1KO siBRCA1 olaparib_300nM 94 2.477121 182.25 0.5157750 2.121324 0.2431383
ALC1KO exp2 si53BP1+siBRCA1 exp2 ALC1KO si53BP1+siBRCA1 ALC1KO si53BP1+siBRCA1 olaparib_300nM 64 2.477121 218.50 0.2929062 2.273009 0.1288627
WT exp3 siCtrl exp3 WT siCtrl WT siCtrl olaparib_300nM 2464 2.477121 2443.50 1.0083896 1.188929 0.8481498
WT exp3 si53BP1 exp3 WT si53BP1 WT si53BP1 olaparib_300nM 2320 2.477121 2369.00 0.9793162 1.265421 0.7739052
WT exp3 siBRCA1 exp3 WT siBRCA1 WT siBRCA1 olaparib_300nM 1020 2.477121 1223.00 0.8340147 1.556467 0.5358382
WT exp3 si53BP1+siBRCA1 exp3 WT si53BP1+siBRCA1 WT si53BP1+siBRCA1 olaparib_300nM 2104 2.477121 2280.00 0.9228070 1.264986 0.7294999
ALC1KO exp3 siCtrl exp3 ALC1KO siCtrl ALC1KO siCtrl olaparib_300nM 812 2.477121 1097.00 0.7402005 2.066197 0.3582430
ALC1KO exp3 si53BP1 exp3 ALC1KO si53BP1 ALC1KO si53BP1 olaparib_300nM 528 2.477121 888.00 0.5945946 1.900335 0.3128893
ALC1KO exp3 siBRCA1 exp3 ALC1KO siBRCA1 ALC1KO siBRCA1 olaparib_300nM 126 2.477121 232.25 0.5425188 2.121324 0.2557454
ALC1KO exp3 si53BP1+siBRCA1 exp3 ALC1KO si53BP1+siBRCA1 ALC1KO si53BP1+siBRCA1 olaparib_300nM 168 2.477121 356.75 0.4709180 2.273009 0.2071782
WT exp4 siCtrl exp4 WT siCtrl WT siCtrl olaparib_300nM 1328 2.477121 1337.00 0.9932685 1.188929 0.8354316
WT exp4 si53BP1 exp4 WT si53BP1 WT si53BP1 olaparib_300nM 1856 2.477121 1745.00 1.0636103 1.265421 0.8405187
WT exp4 siBRCA1 exp4 WT siBRCA1 WT siBRCA1 olaparib_300nM 376 2.477121 421.75 0.8915234 1.556467 0.5727864
WT exp4 si53BP1+siBRCA1 exp4 WT si53BP1+siBRCA1 WT si53BP1+siBRCA1 olaparib_300nM 796 2.477121 996.00 0.7991968 1.264986 0.6317832
ALC1KO exp4 siCtrl exp4 ALC1KO siCtrl ALC1KO siCtrl olaparib_300nM 396 2.477121 555.25 0.7131923 2.066197 0.3451715
ALC1KO exp4 si53BP1 exp4 ALC1KO si53BP1 ALC1KO si53BP1 olaparib_300nM 111 2.477121 175.75 0.6315789 1.900335 0.3323514
ALC1KO exp4 siBRCA1 exp4 ALC1KO siBRCA1 ALC1KO siBRCA1 olaparib_300nM 108 2.477121 230.75 0.4680390 2.121324 0.2206354
ALC1KO exp4 si53BP1+siBRCA1 exp4 ALC1KO si53BP1+siBRCA1 ALC1KO si53BP1+siBRCA1 olaparib_300nM 500 2.477121 735.00 0.6802721 2.273009 0.2992826
WT exp1 siCtrl exp1 WT siCtrl WT siCtrl olaparib_3000nM 1012 3.477121 2029.00 0.4987679 1.188929 0.4195103
WT exp1 si53BP1 exp1 WT si53BP1 WT si53BP1 olaparib_3000nM 796 3.477121 1589.00 0.5009440 1.265421 0.3958713
WT exp1 siBRCA1 exp1 WT siBRCA1 WT siBRCA1 olaparib_3000nM 246 3.477121 654.00 0.3761468 1.556467 0.2416670
WT exp1 si53BP1+siBRCA1 exp1 WT si53BP1+siBRCA1 WT si53BP1+siBRCA1 olaparib_3000nM 468 3.477121 915.00 0.5114754 1.264986 0.4043329
ALC1KO exp1 siCtrl exp1 ALC1KO siCtrl ALC1KO siCtrl olaparib_3000nM 378 3.477121 988.50 0.3823976 2.066197 0.1850732
ALC1KO exp1 si53BP1 exp1 ALC1KO si53BP1 ALC1KO si53BP1 olaparib_3000nM 388 3.477121 847.00 0.4580874 1.900335 0.2410561
ALC1KO exp1 siBRCA1 exp1 ALC1KO siBRCA1 ALC1KO siBRCA1 olaparib_3000nM 71 3.477121 327.75 0.2166285 2.121324 0.1021195
ALC1KO exp1 si53BP1+siBRCA1 exp1 ALC1KO si53BP1+siBRCA1 ALC1KO si53BP1+siBRCA1 olaparib_3000nM 142 3.477121 425.25 0.3339212 2.273009 0.1469071
WT exp2 siCtrl exp2 WT siCtrl WT siCtrl olaparib_3000nM 2084 3.477121 2697.00 0.7727104 1.188929 0.6499216
WT exp2 si53BP1 exp2 WT si53BP1 WT si53BP1 olaparib_3000nM 1886 3.477121 2644.50 0.7131783 1.265421 0.5635896
WT exp2 siBRCA1 exp2 WT siBRCA1 WT siBRCA1 olaparib_3000nM 1020 3.477121 1465.00 0.6962457 1.556467 0.4473243
WT exp2 si53BP1+siBRCA1 exp2 WT si53BP1+siBRCA1 WT si53BP1+siBRCA1 olaparib_3000nM 1832 3.477121 2296.00 0.7979094 1.264986 0.6307655
ALC1KO exp2 siCtrl exp2 ALC1KO siCtrl ALC1KO siCtrl olaparib_3000nM 411 3.477121 998.75 0.4115144 2.066197 0.1991652
ALC1KO exp2 si53BP1 exp2 ALC1KO si53BP1 ALC1KO si53BP1 olaparib_3000nM 416 3.477121 841.00 0.4946492 1.900335 0.2602958
ALC1KO exp2 siBRCA1 exp2 ALC1KO siBRCA1 ALC1KO siBRCA1 olaparib_3000nM 68 3.477121 182.25 0.3731139 2.121324 0.1758873
ALC1KO exp2 si53BP1+siBRCA1 exp2 ALC1KO si53BP1+siBRCA1 ALC1KO si53BP1+siBRCA1 olaparib_3000nM 45 3.477121 218.50 0.2059497 2.273009 0.0906066
WT exp3 siCtrl exp3 WT siCtrl WT siCtrl olaparib_3000nM 1838 3.477121 2443.50 0.7521997 1.188929 0.6326702
WT exp3 si53BP1 exp3 WT si53BP1 WT si53BP1 olaparib_3000nM 1748 3.477121 2369.00 0.7378641 1.265421 0.5830975
WT exp3 siBRCA1 exp3 WT siBRCA1 WT siBRCA1 olaparib_3000nM 768 3.477121 1223.00 0.6279640 1.556467 0.4034546
WT exp3 si53BP1+siBRCA1 exp3 WT si53BP1+siBRCA1 WT si53BP1+siBRCA1 olaparib_3000nM 2064 3.477121 2280.00 0.9052632 1.264986 0.7156311
ALC1KO exp3 siCtrl exp3 ALC1KO siCtrl ALC1KO siCtrl olaparib_3000nM 540 3.477121 1097.00 0.4922516 2.066197 0.2382404
ALC1KO exp3 si53BP1 exp3 ALC1KO si53BP1 ALC1KO si53BP1 olaparib_3000nM 304 3.477121 888.00 0.3423423 1.900335 0.1801484
ALC1KO exp3 siBRCA1 exp3 ALC1KO siBRCA1 ALC1KO siBRCA1 olaparib_3000nM 47 3.477121 232.25 0.2023681 2.121324 0.0953971
ALC1KO exp3 si53BP1+siBRCA1 exp3 ALC1KO si53BP1+siBRCA1 ALC1KO si53BP1+siBRCA1 olaparib_3000nM 75 3.477121 356.75 0.2102313 2.273009 0.0924903
WT exp4 siCtrl exp4 WT siCtrl WT siCtrl olaparib_3000nM 948 3.477121 1337.00 0.7090501 1.188929 0.5963773
WT exp4 si53BP1 exp4 WT si53BP1 WT si53BP1 olaparib_3000nM 1076 3.477121 1745.00 0.6166189 1.265421 0.4872834
WT exp4 siBRCA1 exp4 WT siBRCA1 WT siBRCA1 olaparib_3000nM 191 3.477121 421.75 0.4528749 1.556467 0.2909633
WT exp4 si53BP1+siBRCA1 exp4 WT si53BP1+siBRCA1 WT si53BP1+siBRCA1 olaparib_3000nM 876 3.477121 996.00 0.8795181 1.264986 0.6952790
ALC1KO exp4 siCtrl exp4 ALC1KO siCtrl ALC1KO siCtrl olaparib_3000nM 85 3.477121 555.25 0.1530842 2.066197 0.0740898
ALC1KO exp4 si53BP1 exp4 ALC1KO si53BP1 ALC1KO si53BP1 olaparib_3000nM 38 3.477121 175.75 0.2162162 1.900335 0.1137779
ALC1KO exp4 siBRCA1 exp4 ALC1KO siBRCA1 ALC1KO siBRCA1 olaparib_3000nM 11 3.477121 230.75 0.0476706 2.121324 0.0224721
ALC1KO exp4 si53BP1+siBRCA1 exp4 ALC1KO si53BP1+siBRCA1 ALC1KO si53BP1+siBRCA1 olaparib_3000nM 312 3.477121 735.00 0.4244898 2.273009 0.1867524

Plot Data

library(ggplot2)

# raw data
ggplot(dataset, aes(x=Olaparib, y=Counts)) + 
        theme_bw() +
        theme(panel.grid=element_blank(), text = element_text(size=14)) +
        geom_smooth(method=lm, formula = y ~ poly(x,2), se=FALSE, aes(colour=siRNA)) +
        geom_point(aes(colour=siRNA, shape=Experiment), size=2) +        
        facet_grid(. ~ genotype) +
        xlab(label = "Olaparib (log10 nM)") +
        scale_shape_manual(values=15:19) +
        scale_color_manual(values=c("#000000","#008000","#808080","#008080"))

# NormCounts Linear
ggplot(dataset, aes(x=Olaparib, y=NormCounts, color=siRNA)) + 
        theme_bw() +
        theme(panel.grid=element_blank(), text = element_text(size=14)) +
        geom_point(aes(colour=siRNA), size=2) +        
        geom_smooth(method=lm, formula = y ~ x, se=FALSE) +
        facet_grid(. ~ genotype) +
        xlab(label = "Olaparib (log10 nM)") +
        scale_color_manual(values=c("#000000","#008000","#808080","#008080"))

# NormCounts2 Linear
ggplot(dataset, aes(x=Olaparib, y=NormCounts2, color=siRNA)) + 
        theme_bw() +
        theme(panel.grid=element_blank(), text = element_text(size=14)) +
        geom_point(aes(colour=siRNA), size=2) +        
        geom_smooth(method=lm, formula = y ~ x, se=FALSE) +
        facet_grid(. ~ genotype) +
        xlab(label = "Olaparib (log10 nM)") +
        scale_color_manual(values=c("#000000","#008000","#808080","#008080"))

# NormCounts Quadratic
ggplot(dataset, aes(x=Olaparib, y=NormCounts, color=siRNA)) + 
        theme_bw() +
        theme(panel.grid=element_blank(), text = element_text(size=14)) +
        geom_point(aes(colour=siRNA), size=2) +        
        geom_smooth(method=lm, formula = y ~ poly(x,2), se=FALSE) +
        facet_grid(. ~ genotype) +
        xlab(label = "Olaparib (log10 nM)")+
        scale_color_manual(values=c("#000000","#008000","#808080","#008080")) 

# NormCounts2 Quadratic
ggplot(dataset, aes(x=Olaparib, y=NormCounts2, color=siRNA)) + 
        theme_bw() +
        theme(panel.grid=element_blank(), text = element_text(size=14)) +
        geom_point(aes(colour=siRNA), size=2) +        
        geom_smooth(method=lm, formula = y ~ poly(x,2), se=FALSE) +
        facet_grid(. ~ genotype) +
        xlab(label = "Olaparib (log10 nM)") +
        scale_color_manual(values=c("#000000","#008000","#808080","#008080"))

# NormCounts Cubic
ggplot(dataset, aes(x=Olaparib, y=NormCounts, color=siRNA)) + 
        theme_bw() +
        theme(panel.grid=element_blank(), text = element_text(size=14)) +
        geom_point(aes(colour=siRNA), size=2) +        
        geom_smooth(method=lm, formula = y ~ poly(x,3), se=FALSE) +
        facet_grid(. ~ genotype) +
        xlab(label = "Olaparib (log10 nM)")+
        scale_color_manual(values=c("#000000","#008000","#808080","#008080")) 

# NormCounts2 Cubic
ggplot(dataset, aes(x=Olaparib, y=NormCounts2, color=siRNA)) + 
        theme_bw() +
        theme(panel.grid=element_blank(), text = element_text(size=14)) +
        geom_point(aes(colour=siRNA), size=2) +        
        geom_smooth(method=lm, formula = y ~ poly(x,3), se=FALSE) +
        facet_grid(. ~ genotype) +
        xlab(label = "Olaparib (log10 nM)") +
        scale_color_manual(values=c("#000000","#008000","#808080","#008080"))

library(Cairo)

cairo_pdf("Figure5A.pdf", width = 8, height = 4, family = "Arial")

ggplot(dataset, aes(x=Olaparib, y=NormCounts2)) + 
        theme_bw() +
        theme(panel.grid=element_blank(), text = element_text(size=14)) +
        geom_point(aes(colour = siRNA)) +
        geom_smooth(method=lm, formula = y ~ poly(x,2), se=TRUE, aes(colour = siRNA), fill='#DDDDDD', size=0.5) +
        facet_grid(. ~ genotype) +
        xlab(label = "Olaparib (log10 nM)") +
        ylab(label = "Normalized Counts") +
        scale_color_manual(values=c("#000000","#008000","#808080","#008080"))

dev.off()
## quartz_off_screen 
##                 2

Models

library(MASS)
library(DHARMa)
library(lme4)
library(lmerTest)
library(bbmle)

Linear formula

fit1 <- lm(Counts ~ Experiment + Olaparib*siRNA*genotype, data = dataset)
print(summary(fit1))
## 
## Call:
## lm(formula = Counts ~ Experiment + Olaparib * siRNA * genotype, 
##     data = dataset)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -713.14 -258.88   18.63  224.08  920.16 
## 
## Coefficients:
##                                               Estimate Std. Error t value
## (Intercept)                                   2486.513    167.388  14.855
## Experimentexp2                                 445.938     89.908   4.960
## Experimentexp3                                 389.250     89.908   4.329
## Experimentexp4                                -197.375     89.908  -2.195
## Olaparib                                      -279.540     69.982  -3.994
## siRNAsi53BP1                                    80.926    223.550   0.362
## siRNAsi53BP1+siBRCA1                          -662.557    223.550  -2.964
## siRNAsiBRCA1                                 -1211.136    223.550  -5.418
## genotypeALC1KO                                -938.475    223.550  -4.198
## Olaparib:siRNAsi53BP1                          -64.955     98.969  -0.656
## Olaparib:siRNAsi53BP1+siBRCA1                   84.874     98.969   0.858
## Olaparib:siRNAsiBRCA1                           13.698     98.969   0.138
## Olaparib:genotypeALC1KO                       -149.784     98.969  -1.513
## siRNAsi53BP1:genotypeALC1KO                   -558.350    316.148  -1.766
## siRNAsi53BP1+siBRCA1:genotypeALC1KO           -192.261    316.148  -0.608
## siRNAsiBRCA1:genotypeALC1KO                      5.367    316.148   0.017
## Olaparib:siRNAsi53BP1:genotypeALC1KO           202.473    139.964   1.447
## Olaparib:siRNAsi53BP1+siBRCA1:genotypeALC1KO   119.029    139.964   0.850
## Olaparib:siRNAsiBRCA1:genotypeALC1KO           276.501    139.964   1.976
##                                              Pr(>|t|)    
## (Intercept)                                   < 2e-16 ***
## Experimentexp2                               2.61e-06 ***
## Experimentexp3                               3.33e-05 ***
## Experimentexp4                               0.030262 *  
## Olaparib                                     0.000118 ***
## siRNAsi53BP1                                 0.718051    
## siRNAsi53BP1+siBRCA1                         0.003732 ** 
## siRNAsiBRCA1                                 3.64e-07 ***
## genotypeALC1KO                               5.52e-05 ***
## Olaparib:siRNAsi53BP1                        0.513007    
## Olaparib:siRNAsi53BP1+siBRCA1                0.393008    
## Olaparib:siRNAsiBRCA1                        0.890178    
## Olaparib:genotypeALC1KO                      0.133063    
## siRNAsi53BP1:genotypeALC1KO                  0.080178 .  
## siRNAsi53BP1+siBRCA1:genotypeALC1KO          0.544362    
## siRNAsiBRCA1:genotypeALC1KO                  0.986486    
## Olaparib:siRNAsi53BP1:genotypeALC1KO         0.150876    
## Olaparib:siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.396954    
## Olaparib:siRNAsiBRCA1:genotypeALC1KO         0.050737 .  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 359.6 on 109 degrees of freedom
## Multiple R-squared:  0.8584, Adjusted R-squared:  0.835 
## F-statistic: 36.71 on 18 and 109 DF,  p-value: < 2.2e-16
cat("AIC: ", AIC(fit1))
## AIC:  1889.261
simres <- simulateResiduals(fittedModel = fit1)
plot(simres)

fit2 <- lm(NormCounts ~ Olaparib*siRNA*genotype, data = dataset)
print(summary(fit2))
## 
## Call:
## lm(formula = NormCounts ~ Olaparib * siRNA * genotype, data = dataset)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -0.5166 -0.1169  0.0066  0.1040  0.7429 
## 
## Coefficients:
##                                              Estimate Std. Error t value
## (Intercept)                                   1.25213    0.08809  14.215
## Olaparib                                     -0.13571    0.03900  -3.480
## siRNAsi53BP1                                  0.07162    0.12457   0.575
## siRNAsi53BP1+siBRCA1                          0.01937    0.12457   0.155
## siRNAsiBRCA1                                  0.29335    0.12457   2.355
## genotypeALC1KO                                0.65514    0.12457   5.259
## Olaparib:siRNAsi53BP1                        -0.03855    0.05515  -0.699
## Olaparib:siRNAsi53BP1+siBRCA1                -0.01043    0.05515  -0.189
## Olaparib:siRNAsiBRCA1                        -0.15790    0.05515  -2.863
## Olaparib:genotypeALC1KO                      -0.35263    0.05515  -6.394
## siRNAsi53BP1:genotypeALC1KO                  -0.14870    0.17617  -0.844
## siRNAsi53BP1+siBRCA1:genotypeALC1KO           0.13138    0.17617   0.746
## siRNAsiBRCA1:genotypeALC1KO                  -0.15105    0.17617  -0.857
## Olaparib:siRNAsi53BP1:genotypeALC1KO          0.08004    0.07799   1.026
## Olaparib:siRNAsi53BP1+siBRCA1:genotypeALC1KO -0.07072    0.07799  -0.907
## Olaparib:siRNAsiBRCA1:genotypeALC1KO          0.08131    0.07799   1.042
##                                              Pr(>|t|)    
## (Intercept)                                   < 2e-16 ***
## Olaparib                                     0.000715 ***
## siRNAsi53BP1                                 0.566486    
## siRNAsi53BP1+siBRCA1                         0.876710    
## siRNAsiBRCA1                                 0.020270 *  
## genotypeALC1KO                               7.02e-07 ***
## Olaparib:siRNAsi53BP1                        0.485991    
## Olaparib:siRNAsi53BP1+siBRCA1                0.850393    
## Olaparib:siRNAsiBRCA1                        0.005009 ** 
## Olaparib:genotypeALC1KO                      3.84e-09 ***
## siRNAsi53BP1:genotypeALC1KO                  0.400415    
## siRNAsi53BP1+siBRCA1:genotypeALC1KO          0.457374    
## siRNAsiBRCA1:genotypeALC1KO                  0.393037    
## Olaparib:siRNAsi53BP1:genotypeALC1KO         0.306980    
## Olaparib:siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.366510    
## Olaparib:siRNAsiBRCA1:genotypeALC1KO         0.299436    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 0.2004 on 112 degrees of freedom
## Multiple R-squared:  0.8791, Adjusted R-squared:  0.8629 
## F-statistic: 54.27 on 15 and 112 DF,  p-value: < 2.2e-16
cat("AIC: ", AIC(fit2))
## AIC:  -31.34769
simres <- simulateResiduals(fittedModel = fit2)
plot(simres)

fit3 <- lm(NormCounts2 ~ Olaparib*siRNA*genotype, data = dataset)
print(summary(fit3))
## 
## Call:
## lm(formula = NormCounts2 ~ Olaparib * siRNA * genotype, data = dataset)
## 
## Residuals:
##      Min       1Q   Median       3Q      Max 
## -0.23675 -0.06789  0.00460  0.06796  0.32683 
## 
## Coefficients:
##                                               Estimate Std. Error t value
## (Intercept)                                   1.053158   0.047016  22.400
## Olaparib                                     -0.114146   0.020815  -5.484
## siRNAsi53BP1                                 -0.007063   0.066491  -0.106
## siRNAsi53BP1+siBRCA1                         -0.048008   0.066491  -0.722
## siRNAsiBRCA1                                 -0.060219   0.066491  -0.906
## genotypeALC1KO                               -0.130076   0.066491  -1.956
## Olaparib:siRNAsi53BP1                        -0.023565   0.029437  -0.801
## Olaparib:siRNAsi53BP1+siBRCA1                -0.001379   0.029437  -0.047
## Olaparib:siRNAsiBRCA1                        -0.074492   0.029437  -2.531
## Olaparib:genotypeALC1KO                      -0.122204   0.029437  -4.151
## siRNAsi53BP1:genotypeALC1KO                   0.047067   0.094032   0.501
## siRNAsi53BP1+siBRCA1:genotypeALC1KO           0.030343   0.094032   0.323
## siRNAsiBRCA1:genotypeALC1KO                   0.103308   0.094032   1.099
## Olaparib:siRNAsi53BP1:genotypeALC1KO          0.024770   0.041630   0.595
## Olaparib:siRNAsi53BP1+siBRCA1:genotypeALC1KO -0.012815   0.041630  -0.308
## Olaparib:siRNAsiBRCA1:genotypeALC1KO          0.044529   0.041630   1.070
##                                              Pr(>|t|)    
## (Intercept)                                   < 2e-16 ***
## Olaparib                                     2.61e-07 ***
## siRNAsi53BP1                                   0.9156    
## siRNAsi53BP1+siBRCA1                           0.4718    
## siRNAsiBRCA1                                   0.3671    
## genotypeALC1KO                                 0.0529 .  
## Olaparib:siRNAsi53BP1                          0.4251    
## Olaparib:siRNAsi53BP1+siBRCA1                  0.9627    
## Olaparib:siRNAsiBRCA1                          0.0128 *  
## Olaparib:genotypeALC1KO                      6.47e-05 ***
## siRNAsi53BP1:genotypeALC1KO                    0.6177    
## siRNAsi53BP1+siBRCA1:genotypeALC1KO            0.7475    
## siRNAsiBRCA1:genotypeALC1KO                    0.2743    
## Olaparib:siRNAsi53BP1:genotypeALC1KO           0.5530    
## Olaparib:siRNAsi53BP1+siBRCA1:genotypeALC1KO   0.7588    
## Olaparib:siRNAsiBRCA1:genotypeALC1KO           0.2871    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 0.107 on 112 degrees of freedom
## Multiple R-squared:  0.9007, Adjusted R-squared:  0.8875 
## F-statistic: 67.76 on 15 and 112 DF,  p-value: < 2.2e-16
cat("AIC: ", AIC(fit3))
## AIC:  -192.0674
simres <- simulateResiduals(fittedModel = fit3)
plot(simres)

fit4 <- lmer(Counts ~ Olaparib*siRNA*genotype + (1|UID), data = dataset)
print(summary(fit4))
## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Counts ~ Olaparib * siRNA * genotype + (1 | UID)
##    Data: dataset
## 
## REML criterion at convergence: 1622.4
## 
## Scaled residuals: 
##     Min      1Q  Median      3Q     Max 
## -2.9007 -0.5748 -0.0717  0.5734  2.2507 
## 
## Random effects:
##  Groups   Name        Variance Std.Dev.
##  UID      (Intercept) 197856   444.8   
##  Residual              38460   196.1   
## Number of obs: 128, groups:  UID, 32
## 
## Fixed effects:
##                                               Estimate Std. Error        df
## (Intercept)                                   2645.966    238.525    28.803
## Olaparib                                      -279.540     38.162    88.000
## siRNAsi53BP1                                    80.926    337.326    28.803
## siRNAsi53BP1+siBRCA1                          -662.557    337.326    28.803
## siRNAsiBRCA1                                 -1211.136    337.326    28.803
## genotypeALC1KO                                -938.475    337.326    28.803
## Olaparib:siRNAsi53BP1                          -64.955     53.969    88.000
## Olaparib:siRNAsi53BP1+siBRCA1                   84.874     53.969    88.000
## Olaparib:siRNAsiBRCA1                           13.698     53.969    88.000
## Olaparib:genotypeALC1KO                       -149.784     53.969    88.000
## siRNAsi53BP1:genotypeALC1KO                   -558.350    477.051    28.803
## siRNAsi53BP1+siBRCA1:genotypeALC1KO           -192.261    477.051    28.803
## siRNAsiBRCA1:genotypeALC1KO                      5.367    477.051    28.803
## Olaparib:siRNAsi53BP1:genotypeALC1KO           202.473     76.324    88.000
## Olaparib:siRNAsi53BP1+siBRCA1:genotypeALC1KO   119.029     76.324    88.000
## Olaparib:siRNAsiBRCA1:genotypeALC1KO           276.501     76.324    88.000
##                                              t value Pr(>|t|)    
## (Intercept)                                   11.093 6.50e-12 ***
## Olaparib                                      -7.325 1.08e-10 ***
## siRNAsi53BP1                                   0.240 0.812104    
## siRNAsi53BP1+siBRCA1                          -1.964 0.059229 .  
## siRNAsiBRCA1                                  -3.590 0.001209 ** 
## genotypeALC1KO                                -2.782 0.009428 ** 
## Olaparib:siRNAsi53BP1                         -1.204 0.231992    
## Olaparib:siRNAsi53BP1+siBRCA1                  1.573 0.119393    
## Olaparib:siRNAsiBRCA1                          0.254 0.800239    
## Olaparib:genotypeALC1KO                       -2.775 0.006735 ** 
## siRNAsi53BP1:genotypeALC1KO                   -1.170 0.251425    
## siRNAsi53BP1+siBRCA1:genotypeALC1KO           -0.403 0.689909    
## siRNAsiBRCA1:genotypeALC1KO                    0.011 0.991101    
## Olaparib:siRNAsi53BP1:genotypeALC1KO           2.653 0.009470 ** 
## Olaparib:siRNAsi53BP1+siBRCA1:genotypeALC1KO   1.560 0.122465    
## Olaparib:siRNAsiBRCA1:genotypeALC1KO           3.623 0.000487 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
cat("AIC: ", AIC(fit4))
## AIC:  1658.358
simres <- simulateResiduals(fittedModel = fit4)
plot(simres)

Quadratic formula

fit5 <- lm(Counts ~ Experiment + poly(Olaparib,2)*siRNA*genotype, data = dataset)
print(summary(fit5))
## 
## Call:
## lm(formula = Counts ~ Experiment + poly(Olaparib, 2) * siRNA * 
##     genotype, data = dataset)
## 
## Residuals:
##     Min      1Q  Median      3Q     Max 
## -653.69 -238.10    9.73  216.34  849.41 
## 
## Coefficients:
##                                                        Estimate Std. Error
## (Intercept)                                             1967.17     104.62
## Experimentexp2                                           445.94      89.22
## Experimentexp3                                           389.25      89.22
## Experimentexp4                                          -197.37      89.22
## poly(Olaparib, 2)1                                     -4063.13    1009.39
## poly(Olaparib, 2)2                                     -1834.91    1009.39
## siRNAsi53BP1                                             -39.75     126.17
## siRNAsi53BP1+siBRCA1                                    -504.87     126.17
## siRNAsiBRCA1                                           -1185.69     126.17
## genotypeALC1KO                                         -1216.75     126.17
## poly(Olaparib, 2)1:siRNAsi53BP1                         -944.12    1427.49
## poly(Olaparib, 2)2:siRNAsi53BP1                          302.40    1427.49
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1                 1233.64    1427.49
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1                 1565.84    1427.49
## poly(Olaparib, 2)1:siRNAsiBRCA1                          199.10    1427.49
## poly(Olaparib, 2)2:siRNAsiBRCA1                         2351.59    1427.49
## poly(Olaparib, 2)1:genotypeALC1KO                      -2177.12    1427.49
## poly(Olaparib, 2)2:genotypeALC1KO                       3444.07    1427.49
## siRNAsi53BP1:genotypeALC1KO                             -182.19     178.44
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                       28.87     178.44
## siRNAsiBRCA1:genotypeALC1KO                              519.06     178.44
## poly(Olaparib, 2)1:siRNAsi53BP1:genotypeALC1KO          2942.95    2018.78
## poly(Olaparib, 2)2:siRNAsi53BP1:genotypeALC1KO         -1295.71    2018.78
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO  1730.08    2018.78
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO -2295.16    2018.78
## poly(Olaparib, 2)1:siRNAsiBRCA1:genotypeALC1KO          4018.95    2018.78
## poly(Olaparib, 2)2:siRNAsiBRCA1:genotypeALC1KO         -3685.15    2018.78
##                                                        t value Pr(>|t|)    
## (Intercept)                                             18.803  < 2e-16 ***
## Experimentexp2                                           4.998 2.44e-06 ***
## Experimentexp3                                           4.363 3.10e-05 ***
## Experimentexp4                                          -2.212  0.02920 *  
## poly(Olaparib, 2)1                                      -4.025  0.00011 ***
## poly(Olaparib, 2)2                                      -1.818  0.07205 .  
## siRNAsi53BP1                                            -0.315  0.75338    
## siRNAsi53BP1+siBRCA1                                    -4.001  0.00012 ***
## siRNAsiBRCA1                                            -9.397 1.91e-15 ***
## genotypeALC1KO                                          -9.643 5.48e-16 ***
## poly(Olaparib, 2)1:siRNAsi53BP1                         -0.661  0.50987    
## poly(Olaparib, 2)2:siRNAsi53BP1                          0.212  0.83266    
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1                  0.864  0.38952    
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1                  1.097  0.27529    
## poly(Olaparib, 2)1:siRNAsiBRCA1                          0.139  0.88936    
## poly(Olaparib, 2)2:siRNAsiBRCA1                          1.647  0.10259    
## poly(Olaparib, 2)1:genotypeALC1KO                       -1.525  0.13035    
## poly(Olaparib, 2)2:genotypeALC1KO                        2.413  0.01764 *  
## siRNAsi53BP1:genotypeALC1KO                             -1.021  0.30968    
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                      0.162  0.87177    
## siRNAsiBRCA1:genotypeALC1KO                              2.909  0.00446 ** 
## poly(Olaparib, 2)1:siRNAsi53BP1:genotypeALC1KO           1.458  0.14800    
## poly(Olaparib, 2)2:siRNAsi53BP1:genotypeALC1KO          -0.642  0.52244    
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO   0.857  0.39348    
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO  -1.137  0.25827    
## poly(Olaparib, 2)1:siRNAsiBRCA1:genotypeALC1KO           1.991  0.04921 *  
## poly(Olaparib, 2)2:siRNAsiBRCA1:genotypeALC1KO          -1.825  0.07089 .  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 356.9 on 101 degrees of freedom
## Multiple R-squared:  0.8708, Adjusted R-squared:  0.8375 
## F-statistic: 26.18 on 26 and 101 DF,  p-value: < 2.2e-16
cat("AIC: ", AIC(fit5))
## AIC:  1893.534
simres <- simulateResiduals(fittedModel = fit5)
plot(simres)

fit6 <- lm(NormCounts ~ poly(Olaparib,2)*siRNA*genotype, data = dataset)
print(summary(fit6))
## 
## Call:
## lm(formula = NormCounts ~ poly(Olaparib, 2) * siRNA * genotype, 
##     data = dataset)
## 
## Residuals:
##      Min       1Q   Median       3Q      Max 
## -0.49865 -0.08137  0.00024  0.08742  0.54005 
## 
## Coefficients:
##                                                          Estimate Std. Error
## (Intercept)                                             1.000e+00  4.146e-02
## poly(Olaparib, 2)1                                     -1.973e+00  4.691e-01
## poly(Olaparib, 2)2                                     -8.808e-01  4.691e-01
## siRNAsi53BP1                                           -2.231e-16  5.864e-02
## siRNAsi53BP1+siBRCA1                                    1.601e-16  5.864e-02
## siRNAsiBRCA1                                            2.393e-17  5.864e-02
## genotypeALC1KO                                         -6.681e-16  5.864e-02
## poly(Olaparib, 2)1:siRNAsi53BP1                        -5.603e-01  6.634e-01
## poly(Olaparib, 2)2:siRNAsi53BP1                         1.255e-01  6.634e-01
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1                -1.515e-01  6.634e-01
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1                 8.736e-01  6.634e-01
## poly(Olaparib, 2)1:siRNAsiBRCA1                        -2.295e+00  6.634e-01
## poly(Olaparib, 2)2:siRNAsiBRCA1                         1.021e+00  6.634e-01
## poly(Olaparib, 2)1:genotypeALC1KO                      -5.126e+00  6.634e-01
## poly(Olaparib, 2)2:genotypeALC1KO                       2.709e+00  6.634e-01
## siRNAsi53BP1:genotypeALC1KO                             1.460e-16  8.292e-02
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                    -2.043e-16  8.292e-02
## siRNAsiBRCA1:genotypeALC1KO                            -4.197e-17  8.292e-02
## poly(Olaparib, 2)1:siRNAsi53BP1:genotypeALC1KO          1.163e+00  9.382e-01
## poly(Olaparib, 2)2:siRNAsi53BP1:genotypeALC1KO         -1.002e+00  9.382e-01
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO -1.028e+00  9.382e-01
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO -1.787e-01  9.382e-01
## poly(Olaparib, 2)1:siRNAsiBRCA1:genotypeALC1KO          1.182e+00  9.382e-01
## poly(Olaparib, 2)2:siRNAsiBRCA1:genotypeALC1KO         -1.788e+00  9.382e-01
##                                                        t value Pr(>|t|)    
## (Intercept)                                             24.119  < 2e-16 ***
## poly(Olaparib, 2)1                                      -4.205 5.54e-05 ***
## poly(Olaparib, 2)2                                      -1.878 0.063219 .  
## siRNAsi53BP1                                             0.000 1.000000    
## siRNAsi53BP1+siBRCA1                                     0.000 1.000000    
## siRNAsiBRCA1                                             0.000 1.000000    
## genotypeALC1KO                                           0.000 1.000000    
## poly(Olaparib, 2)1:siRNAsi53BP1                         -0.845 0.400241    
## poly(Olaparib, 2)2:siRNAsi53BP1                          0.189 0.850307    
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1                 -0.228 0.819750    
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1                  1.317 0.190765    
## poly(Olaparib, 2)1:siRNAsiBRCA1                         -3.460 0.000786 ***
## poly(Olaparib, 2)2:siRNAsiBRCA1                          1.539 0.126825    
## poly(Olaparib, 2)1:genotypeALC1KO                       -7.726 7.25e-12 ***
## poly(Olaparib, 2)2:genotypeALC1KO                        4.083 8.75e-05 ***
## siRNAsi53BP1:genotypeALC1KO                              0.000 1.000000    
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                      0.000 1.000000    
## siRNAsiBRCA1:genotypeALC1KO                              0.000 1.000000    
## poly(Olaparib, 2)1:siRNAsi53BP1:genotypeALC1KO           1.240 0.217734    
## poly(Olaparib, 2)2:siRNAsi53BP1:genotypeALC1KO          -1.068 0.288079    
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO  -1.096 0.275776    
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO  -0.191 0.849282    
## poly(Olaparib, 2)1:siRNAsiBRCA1:genotypeALC1KO           1.260 0.210604    
## poly(Olaparib, 2)2:siRNAsiBRCA1:genotypeALC1KO          -1.906 0.059369 .  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 0.1658 on 104 degrees of freedom
## Multiple R-squared:  0.9231, Adjusted R-squared:  0.9061 
## F-statistic: 54.27 on 23 and 104 DF,  p-value: < 2.2e-16
cat("AIC: ", AIC(fit6))
## AIC:  -73.28383
simres <- simulateResiduals(fittedModel = fit6)
plot(simres)

fit7 <- lm(NormCounts2 ~ poly(Olaparib,2)*siRNA*genotype, data = dataset)
print(summary(fit7))
## 
## Call:
## lm(formula = NormCounts2 ~ poly(Olaparib, 2) * siRNA * genotype, 
##     data = dataset)
## 
## Residuals:
##       Min        1Q    Median        3Q       Max 
## -0.235066 -0.048533  0.000176  0.053866  0.242777 
## 
## Coefficients:
##                                                         Estimate Std. Error
## (Intercept)                                             0.841093   0.022641
## poly(Olaparib, 2)1                                     -1.659109   0.256151
## poly(Olaparib, 2)2                                     -0.740846   0.256151
## siRNAsi53BP1                                           -0.050843   0.032019
## siRNAsi53BP1+siBRCA1                                   -0.050571   0.032019
## siRNAsiBRCA1                                           -0.198613   0.032019
## genotypeALC1KO                                         -0.357112   0.032019
## poly(Olaparib, 2)1:siRNAsi53BP1                        -0.342512   0.362252
## poly(Olaparib, 2)2:siRNAsi53BP1                         0.143967   0.362252
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1                -0.020047   0.362252
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1                 0.735155   0.362252
## poly(Olaparib, 2)1:siRNAsiBRCA1                        -1.082742   0.362252
## poly(Olaparib, 2)2:siRNAsiBRCA1                         0.830908   0.362252
## poly(Olaparib, 2)1:genotypeALC1KO                      -1.776242   0.362252
## poly(Olaparib, 2)2:genotypeALC1KO                       1.625433   0.362252
## siRNAsi53BP1:genotypeALC1KO                             0.093085   0.045281
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                     0.006535   0.045281
## siRNAsiBRCA1:genotypeALC1KO                             0.186036   0.045281
## poly(Olaparib, 2)1:siRNAsi53BP1:genotypeALC1KO          0.360026   0.512301
## poly(Olaparib, 2)2:siRNAsi53BP1:genotypeALC1KO         -0.527875   0.512301
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO -0.186264   0.512301
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO -0.509928   0.512301
## poly(Olaparib, 2)1:siRNAsiBRCA1:genotypeALC1KO          0.647226   0.512301
## poly(Olaparib, 2)2:siRNAsiBRCA1:genotypeALC1KO         -1.215675   0.512301
##                                                        t value Pr(>|t|)    
## (Intercept)                                             37.150  < 2e-16 ***
## poly(Olaparib, 2)1                                      -6.477 3.16e-09 ***
## poly(Olaparib, 2)2                                      -2.892  0.00466 ** 
## siRNAsi53BP1                                            -1.588  0.11534    
## siRNAsi53BP1+siBRCA1                                    -1.579  0.11728    
## siRNAsiBRCA1                                            -6.203 1.14e-08 ***
## genotypeALC1KO                                         -11.153  < 2e-16 ***
## poly(Olaparib, 2)1:siRNAsi53BP1                         -0.946  0.34659    
## poly(Olaparib, 2)2:siRNAsi53BP1                          0.397  0.69187    
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1                 -0.055  0.95597    
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1                  2.029  0.04497 *  
## poly(Olaparib, 2)1:siRNAsiBRCA1                         -2.989  0.00349 ** 
## poly(Olaparib, 2)2:siRNAsiBRCA1                          2.294  0.02382 *  
## poly(Olaparib, 2)1:genotypeALC1KO                       -4.903 3.49e-06 ***
## poly(Olaparib, 2)2:genotypeALC1KO                        4.487 1.87e-05 ***
## siRNAsi53BP1:genotypeALC1KO                              2.056  0.04232 *  
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                      0.144  0.88553    
## siRNAsiBRCA1:genotypeALC1KO                              4.108 7.96e-05 ***
## poly(Olaparib, 2)1:siRNAsi53BP1:genotypeALC1KO           0.703  0.48377    
## poly(Olaparib, 2)2:siRNAsi53BP1:genotypeALC1KO          -1.030  0.30521    
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO  -0.364  0.71691    
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO  -0.995  0.32187    
## poly(Olaparib, 2)1:siRNAsiBRCA1:genotypeALC1KO           1.263  0.20928    
## poly(Olaparib, 2)2:siRNAsiBRCA1:genotypeALC1KO          -2.373  0.01948 *  
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 0.09056 on 104 degrees of freedom
## Multiple R-squared:  0.9339, Adjusted R-squared:  0.9193 
## F-statistic: 63.92 on 23 and 104 DF,  p-value: < 2.2e-16
cat("AIC: ", AIC(fit7))
## AIC:  -228.1676
simres <- simulateResiduals(fittedModel = fit7)
plot(simres)

fit8 <- lmer(Counts ~ poly(Olaparib,2)*siRNA*genotype + (1|UID), data = dataset)
print(summary(fit8))
## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Counts ~ poly(Olaparib, 2) * siRNA * genotype + (1 | UID)
##    Data: dataset
## 
## REML criterion at convergence: 1427.1
## 
## Scaled residuals: 
##      Min       1Q   Median       3Q      Max 
## -2.52515 -0.47579 -0.02532  0.47074  2.39428 
## 
## Random effects:
##  Groups   Name        Variance Std.Dev.
##  UID      (Intercept) 200751   448.1   
##  Residual              26878   163.9   
## Number of obs: 128, groups:  UID, 32
## 
## Fixed effects:
##                                                        Estimate Std. Error
## (Intercept)                                             2126.62     227.74
## poly(Olaparib, 2)1                                     -4063.13     463.71
## poly(Olaparib, 2)2                                     -1834.91     463.71
## siRNAsi53BP1                                             -39.75     322.08
## siRNAsi53BP1+siBRCA1                                    -504.87     322.08
## siRNAsiBRCA1                                           -1185.69     322.08
## genotypeALC1KO                                         -1216.75     322.08
## poly(Olaparib, 2)1:siRNAsi53BP1                         -944.12     655.78
## poly(Olaparib, 2)2:siRNAsi53BP1                          302.40     655.78
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1                 1233.64     655.78
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1                 1565.84     655.78
## poly(Olaparib, 2)1:siRNAsiBRCA1                          199.10     655.78
## poly(Olaparib, 2)2:siRNAsiBRCA1                         2351.59     655.78
## poly(Olaparib, 2)1:genotypeALC1KO                      -2177.12     655.78
## poly(Olaparib, 2)2:genotypeALC1KO                       3444.07     655.78
## siRNAsi53BP1:genotypeALC1KO                             -182.19     455.49
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                       28.87     455.49
## siRNAsiBRCA1:genotypeALC1KO                              519.06     455.49
## poly(Olaparib, 2)1:siRNAsi53BP1:genotypeALC1KO          2942.95     927.42
## poly(Olaparib, 2)2:siRNAsi53BP1:genotypeALC1KO         -1295.71     927.42
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO  1730.08     927.42
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO -2295.16     927.42
## poly(Olaparib, 2)1:siRNAsiBRCA1:genotypeALC1KO          4018.95     927.42
## poly(Olaparib, 2)2:siRNAsiBRCA1:genotypeALC1KO         -3685.15     927.42
##                                                              df t value
## (Intercept)                                               24.00   9.338
## poly(Olaparib, 2)1                                        80.00  -8.762
## poly(Olaparib, 2)2                                        80.00  -3.957
## siRNAsi53BP1                                              24.00  -0.123
## siRNAsi53BP1+siBRCA1                                      24.00  -1.568
## siRNAsiBRCA1                                              24.00  -3.681
## genotypeALC1KO                                            24.00  -3.778
## poly(Olaparib, 2)1:siRNAsi53BP1                           80.00  -1.440
## poly(Olaparib, 2)2:siRNAsi53BP1                           80.00   0.461
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1                   80.00   1.881
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1                   80.00   2.388
## poly(Olaparib, 2)1:siRNAsiBRCA1                           80.00   0.304
## poly(Olaparib, 2)2:siRNAsiBRCA1                           80.00   3.586
## poly(Olaparib, 2)1:genotypeALC1KO                         80.00  -3.320
## poly(Olaparib, 2)2:genotypeALC1KO                         80.00   5.252
## siRNAsi53BP1:genotypeALC1KO                               24.00  -0.400
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                       24.00   0.063
## siRNAsiBRCA1:genotypeALC1KO                               24.00   1.140
## poly(Olaparib, 2)1:siRNAsi53BP1:genotypeALC1KO            80.00   3.173
## poly(Olaparib, 2)2:siRNAsi53BP1:genotypeALC1KO            80.00  -1.397
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO    80.00   1.865
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO    80.00  -2.475
## poly(Olaparib, 2)1:siRNAsiBRCA1:genotypeALC1KO            80.00   4.333
## poly(Olaparib, 2)2:siRNAsiBRCA1:genotypeALC1KO            80.00  -3.974
##                                                        Pr(>|t|)    
## (Intercept)                                            1.84e-09 ***
## poly(Olaparib, 2)1                                     2.58e-13 ***
## poly(Olaparib, 2)2                                     0.000163 ***
## siRNAsi53BP1                                           0.902805    
## siRNAsi53BP1+siBRCA1                                   0.130079    
## siRNAsiBRCA1                                           0.001174 ** 
## genotypeALC1KO                                         0.000922 ***
## poly(Olaparib, 2)1:siRNAsi53BP1                        0.153859    
## poly(Olaparib, 2)2:siRNAsi53BP1                        0.645960    
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1                0.063586 .  
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1                0.019310 *  
## poly(Olaparib, 2)1:siRNAsiBRCA1                        0.762222    
## poly(Olaparib, 2)2:siRNAsiBRCA1                        0.000576 ***
## poly(Olaparib, 2)1:genotypeALC1KO                      0.001358 ** 
## poly(Olaparib, 2)2:genotypeALC1KO                      1.21e-06 ***
## siRNAsi53BP1:genotypeALC1KO                            0.692708    
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                    0.949978    
## siRNAsiBRCA1:genotypeALC1KO                            0.265711    
## poly(Olaparib, 2)1:siRNAsi53BP1:genotypeALC1KO         0.002139 ** 
## poly(Olaparib, 2)2:siRNAsi53BP1:genotypeALC1KO         0.166242    
## poly(Olaparib, 2)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.065780 .  
## poly(Olaparib, 2)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.015446 *  
## poly(Olaparib, 2)1:siRNAsiBRCA1:genotypeALC1KO         4.23e-05 ***
## poly(Olaparib, 2)2:siRNAsiBRCA1:genotypeALC1KO         0.000154 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
cat("AIC: ", AIC(fit8))
## AIC:  1479.072
simres <- simulateResiduals(fittedModel = fit8)
plot(simres)

Cubic formula

fit9 <- lm(Counts ~ Experiment + poly(Olaparib,3)*siRNA*genotype, data = dataset)
print(summary(fit9))
## 
## Call:
## lm(formula = Counts ~ Experiment + poly(Olaparib, 3) * siRNA * 
##     genotype, data = dataset)
## 
## Residuals:
##    Min     1Q Median     3Q    Max 
## -682.5 -229.8   16.2  210.0  844.8 
## 
## Coefficients:
##                                                        Estimate Std. Error
## (Intercept)                                             1967.17     108.46
## Experimentexp2                                           445.94      92.49
## Experimentexp3                                           389.25      92.49
## Experimentexp4                                          -197.37      92.49
## poly(Olaparib, 3)1                                     -4063.13    1046.45
## poly(Olaparib, 3)2                                     -1834.91    1046.45
## poly(Olaparib, 3)3                                      -658.33    1046.45
## siRNAsi53BP1                                             -39.75     130.81
## siRNAsi53BP1+siBRCA1                                    -504.87     130.81
## siRNAsiBRCA1                                           -1185.69     130.81
## genotypeALC1KO                                         -1216.75     130.81
## poly(Olaparib, 3)1:siRNAsi53BP1                         -944.12    1479.91
## poly(Olaparib, 3)2:siRNAsi53BP1                          302.40    1479.91
## poly(Olaparib, 3)3:siRNAsi53BP1                          486.10    1479.91
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1                 1233.64    1479.91
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1                 1565.84    1479.91
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1                 1284.68    1479.91
## poly(Olaparib, 3)1:siRNAsiBRCA1                          199.10    1479.91
## poly(Olaparib, 3)2:siRNAsiBRCA1                         2351.59    1479.91
## poly(Olaparib, 3)3:siRNAsiBRCA1                          593.91    1479.91
## poly(Olaparib, 3)1:genotypeALC1KO                      -2177.12    1479.91
## poly(Olaparib, 3)2:genotypeALC1KO                       3444.07    1479.91
## poly(Olaparib, 3)3:genotypeALC1KO                        375.79    1479.91
## siRNAsi53BP1:genotypeALC1KO                             -182.19     184.99
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                       28.87     184.99
## siRNAsiBRCA1:genotypeALC1KO                              519.06     184.99
## poly(Olaparib, 3)1:siRNAsi53BP1:genotypeALC1KO          2942.95    2092.91
## poly(Olaparib, 3)2:siRNAsi53BP1:genotypeALC1KO         -1295.71    2092.91
## poly(Olaparib, 3)3:siRNAsi53BP1:genotypeALC1KO            77.89    2092.91
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO  1730.08    2092.91
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO -2295.16    2092.91
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1:genotypeALC1KO -1183.92    2092.91
## poly(Olaparib, 3)1:siRNAsiBRCA1:genotypeALC1KO          4018.95    2092.91
## poly(Olaparib, 3)2:siRNAsiBRCA1:genotypeALC1KO         -3685.15    2092.91
## poly(Olaparib, 3)3:siRNAsiBRCA1:genotypeALC1KO          -196.83    2092.91
##                                                        t value Pr(>|t|)    
## (Intercept)                                             18.137  < 2e-16 ***
## Experimentexp2                                           4.821 5.55e-06 ***
## Experimentexp3                                           4.208 5.93e-05 ***
## Experimentexp4                                          -2.134 0.035481 *  
## poly(Olaparib, 3)1                                      -3.883 0.000193 ***
## poly(Olaparib, 3)2                                      -1.753 0.082819 .  
## poly(Olaparib, 3)3                                      -0.629 0.530825    
## siRNAsi53BP1                                            -0.304 0.761896    
## siRNAsi53BP1+siBRCA1                                    -3.860 0.000209 ***
## siRNAsiBRCA1                                            -9.064 1.95e-14 ***
## genotypeALC1KO                                          -9.302 6.14e-15 ***
## poly(Olaparib, 3)1:siRNAsi53BP1                         -0.638 0.525069    
## poly(Olaparib, 3)2:siRNAsi53BP1                          0.204 0.838538    
## poly(Olaparib, 3)3:siRNAsi53BP1                          0.328 0.743300    
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1                  0.834 0.406646    
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1                  1.058 0.292766    
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1                  0.868 0.387587    
## poly(Olaparib, 3)1:siRNAsiBRCA1                          0.135 0.893273    
## poly(Olaparib, 3)2:siRNAsiBRCA1                          1.589 0.115452    
## poly(Olaparib, 3)3:siRNAsiBRCA1                          0.401 0.689108    
## poly(Olaparib, 3)1:genotypeALC1KO                       -1.471 0.144636    
## poly(Olaparib, 3)2:genotypeALC1KO                        2.327 0.022124 *  
## poly(Olaparib, 3)3:genotypeALC1KO                        0.254 0.800114    
## siRNAsi53BP1:genotypeALC1KO                             -0.985 0.327250    
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                      0.156 0.876300    
## siRNAsiBRCA1:genotypeALC1KO                              2.806 0.006111 ** 
## poly(Olaparib, 3)1:siRNAsi53BP1:genotypeALC1KO           1.406 0.163011    
## poly(Olaparib, 3)2:siRNAsi53BP1:genotypeALC1KO          -0.619 0.537367    
## poly(Olaparib, 3)3:siRNAsi53BP1:genotypeALC1KO           0.037 0.970393    
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO   0.827 0.410557    
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO  -1.097 0.275632    
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1:genotypeALC1KO  -0.566 0.572973    
## poly(Olaparib, 3)1:siRNAsiBRCA1:genotypeALC1KO           1.920 0.057888 .  
## poly(Olaparib, 3)2:siRNAsiBRCA1:genotypeALC1KO          -1.761 0.081563 .  
## poly(Olaparib, 3)3:siRNAsiBRCA1:genotypeALC1KO          -0.094 0.925276    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 370 on 93 degrees of freedom
## Multiple R-squared:  0.8721, Adjusted R-squared:  0.8254 
## F-statistic: 18.66 on 34 and 93 DF,  p-value: < 2.2e-16
cat("AIC: ", AIC(fit9))
## AIC:  1908.202
simres <- simulateResiduals(fittedModel = fit9)
plot(simres)

fit10 <- lm(NormCounts ~ poly(Olaparib,3)*siRNA*genotype, data = dataset)
print(summary(fit10))
## 
## Call:
## lm(formula = NormCounts ~ poly(Olaparib, 3) * siRNA * genotype, 
##     data = dataset)
## 
## Residuals:
##      Min       1Q   Median       3Q      Max 
## -0.48516 -0.08021  0.00374  0.08583  0.52791 
## 
## Coefficients:
##                                                          Estimate Std. Error
## (Intercept)                                             1.000e+00  4.223e-02
## poly(Olaparib, 3)1                                     -1.973e+00  4.778e-01
## poly(Olaparib, 3)2                                     -8.808e-01  4.778e-01
## poly(Olaparib, 3)3                                     -3.028e-01  4.778e-01
## siRNAsi53BP1                                            8.493e-17  5.973e-02
## siRNAsi53BP1+siBRCA1                                    3.307e-16  5.973e-02
## siRNAsiBRCA1                                           -6.790e-17  5.973e-02
## genotypeALC1KO                                         -5.075e-16  5.973e-02
## poly(Olaparib, 3)1:siRNAsi53BP1                        -5.603e-01  6.757e-01
## poly(Olaparib, 3)2:siRNAsi53BP1                         1.255e-01  6.757e-01
## poly(Olaparib, 3)3:siRNAsi53BP1                         2.073e-01  6.757e-01
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1                -1.515e-01  6.757e-01
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1                 8.736e-01  6.757e-01
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1                 5.385e-01  6.757e-01
## poly(Olaparib, 3)1:siRNAsiBRCA1                        -2.295e+00  6.757e-01
## poly(Olaparib, 3)2:siRNAsiBRCA1                         1.021e+00  6.757e-01
## poly(Olaparib, 3)3:siRNAsiBRCA1                         3.140e-01  6.757e-01
## poly(Olaparib, 3)1:genotypeALC1KO                      -5.126e+00  6.757e-01
## poly(Olaparib, 3)2:genotypeALC1KO                       2.709e+00  6.757e-01
## poly(Olaparib, 3)3:genotypeALC1KO                      -1.721e-01  6.757e-01
## siRNAsi53BP1:genotypeALC1KO                            -3.885e-17  8.447e-02
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                    -4.261e-16  8.447e-02
## siRNAsiBRCA1:genotypeALC1KO                            -1.683e-16  8.447e-02
## poly(Olaparib, 3)1:siRNAsi53BP1:genotypeALC1KO          1.163e+00  9.557e-01
## poly(Olaparib, 3)2:siRNAsi53BP1:genotypeALC1KO         -1.002e+00  9.557e-01
## poly(Olaparib, 3)3:siRNAsi53BP1:genotypeALC1KO          5.200e-01  9.557e-01
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO -1.028e+00  9.557e-01
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO -1.787e-01  9.557e-01
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1:genotypeALC1KO -5.458e-01  9.557e-01
## poly(Olaparib, 3)1:siRNAsiBRCA1:genotypeALC1KO          1.182e+00  9.557e-01
## poly(Olaparib, 3)2:siRNAsiBRCA1:genotypeALC1KO         -1.788e+00  9.557e-01
## poly(Olaparib, 3)3:siRNAsiBRCA1:genotypeALC1KO          6.968e-01  9.557e-01
##                                                        t value Pr(>|t|)    
## (Intercept)                                             23.677  < 2e-16 ***
## poly(Olaparib, 3)1                                      -4.128 7.80e-05 ***
## poly(Olaparib, 3)2                                      -1.843 0.068359 .  
## poly(Olaparib, 3)3                                      -0.634 0.527770    
## siRNAsi53BP1                                             0.000 1.000000    
## siRNAsi53BP1+siBRCA1                                     0.000 1.000000    
## siRNAsiBRCA1                                             0.000 1.000000    
## genotypeALC1KO                                           0.000 1.000000    
## poly(Olaparib, 3)1:siRNAsi53BP1                         -0.829 0.409047    
## poly(Olaparib, 3)2:siRNAsi53BP1                          0.186 0.853045    
## poly(Olaparib, 3)3:siRNAsi53BP1                          0.307 0.759698    
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1                 -0.224 0.823029    
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1                  1.293 0.199180    
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1                  0.797 0.427501    
## poly(Olaparib, 3)1:siRNAsiBRCA1                         -3.396 0.000995 ***
## poly(Olaparib, 3)2:siRNAsiBRCA1                          1.511 0.134098    
## poly(Olaparib, 3)3:siRNAsiBRCA1                          0.465 0.643245    
## poly(Olaparib, 3)1:genotypeALC1KO                       -7.585 2.12e-11 ***
## poly(Olaparib, 3)2:genotypeALC1KO                        4.008 0.000121 ***
## poly(Olaparib, 3)3:genotypeALC1KO                       -0.255 0.799459    
## siRNAsi53BP1:genotypeALC1KO                              0.000 1.000000    
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                      0.000 1.000000    
## siRNAsiBRCA1:genotypeALC1KO                              0.000 1.000000    
## poly(Olaparib, 3)1:siRNAsi53BP1:genotypeALC1KO           1.217 0.226438    
## poly(Olaparib, 3)2:siRNAsi53BP1:genotypeALC1KO          -1.048 0.297146    
## poly(Olaparib, 3)3:siRNAsi53BP1:genotypeALC1KO           0.544 0.587587    
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO  -1.076 0.284814    
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO  -0.187 0.852038    
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1:genotypeALC1KO  -0.571 0.569225    
## poly(Olaparib, 3)1:siRNAsiBRCA1:genotypeALC1KO           1.237 0.219241    
## poly(Olaparib, 3)2:siRNAsiBRCA1:genotypeALC1KO          -1.871 0.064330 .  
## poly(Olaparib, 3)3:siRNAsiBRCA1:genotypeALC1KO           0.729 0.467676    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 0.1689 on 96 degrees of freedom
## Multiple R-squared:  0.9263, Adjusted R-squared:  0.9025 
## F-statistic: 38.94 on 31 and 96 DF,  p-value: < 2.2e-16
cat("AIC: ", AIC(fit10))
## AIC:  -62.8016
simres <- simulateResiduals(fittedModel = fit10)
plot(simres)

fit11 <- lm(NormCounts2 ~ poly(Olaparib,3)*siRNA*genotype, data = dataset)
print(summary(fit11))
## 
## Call:
## lm(formula = NormCounts2 ~ poly(Olaparib, 3) * siRNA * genotype, 
##     data = dataset)
## 
## Residuals:
##       Min        1Q    Median        3Q       Max 
## -0.228704 -0.042322  0.002445  0.054386  0.232250 
## 
## Coefficients:
##                                                         Estimate Std. Error
## (Intercept)                                             0.841093   0.023068
## poly(Olaparib, 3)1                                     -1.659109   0.260990
## poly(Olaparib, 3)2                                     -0.740846   0.260990
## poly(Olaparib, 3)3                                     -0.254690   0.260990
## siRNAsi53BP1                                           -0.050843   0.032624
## siRNAsi53BP1+siBRCA1                                   -0.050571   0.032624
## siRNAsiBRCA1                                           -0.198613   0.032624
## genotypeALC1KO                                         -0.357112   0.032624
## poly(Olaparib, 3)1:siRNAsi53BP1                        -0.342512   0.369096
## poly(Olaparib, 3)2:siRNAsi53BP1                         0.143967   0.369096
## poly(Olaparib, 3)3:siRNAsi53BP1                         0.179203   0.369096
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1                -0.020047   0.369096
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1                 0.735155   0.369096
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1                 0.440989   0.369096
## poly(Olaparib, 3)1:siRNAsiBRCA1                        -1.082742   0.369096
## poly(Olaparib, 3)2:siRNAsiBRCA1                         0.830908   0.369096
## poly(Olaparib, 3)3:siRNAsiBRCA1                         0.261866   0.369096
## poly(Olaparib, 3)1:genotypeALC1KO                      -1.776242   0.369096
## poly(Olaparib, 3)2:genotypeALC1KO                       1.625433   0.369096
## poly(Olaparib, 3)3:genotypeALC1KO                       0.024820   0.369096
## siRNAsi53BP1:genotypeALC1KO                             0.093085   0.046137
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                     0.006535   0.046137
## siRNAsiBRCA1:genotypeALC1KO                             0.186036   0.046137
## poly(Olaparib, 3)1:siRNAsi53BP1:genotypeALC1KO          0.360026   0.521980
## poly(Olaparib, 3)2:siRNAsi53BP1:genotypeALC1KO         -0.527875   0.521980
## poly(Olaparib, 3)3:siRNAsi53BP1:genotypeALC1KO          0.183467   0.521980
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO -0.186264   0.521980
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO -0.509928   0.521980
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1:genotypeALC1KO -0.423311   0.521980
## poly(Olaparib, 3)1:siRNAsiBRCA1:genotypeALC1KO          0.647226   0.521980
## poly(Olaparib, 3)2:siRNAsiBRCA1:genotypeALC1KO         -1.215675   0.521980
## poly(Olaparib, 3)3:siRNAsiBRCA1:genotypeALC1KO          0.220606   0.521980
##                                                        t value Pr(>|t|)    
## (Intercept)                                             36.461  < 2e-16 ***
## poly(Olaparib, 3)1                                      -6.357 6.92e-09 ***
## poly(Olaparib, 3)2                                      -2.839 0.005530 ** 
## poly(Olaparib, 3)3                                      -0.976 0.331586    
## siRNAsi53BP1                                            -1.558 0.122415    
## siRNAsi53BP1+siBRCA1                                    -1.550 0.124404    
## siRNAsiBRCA1                                            -6.088 2.35e-08 ***
## genotypeALC1KO                                         -10.946  < 2e-16 ***
## poly(Olaparib, 3)1:siRNAsi53BP1                         -0.928 0.355747    
## poly(Olaparib, 3)2:siRNAsi53BP1                          0.390 0.697361    
## poly(Olaparib, 3)3:siRNAsi53BP1                          0.486 0.628414    
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1                 -0.054 0.956799    
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1                  1.992 0.049237 *  
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1                  1.195 0.235116    
## poly(Olaparib, 3)1:siRNAsiBRCA1                         -2.933 0.004192 ** 
## poly(Olaparib, 3)2:siRNAsiBRCA1                          2.251 0.026654 *  
## poly(Olaparib, 3)3:siRNAsiBRCA1                          0.709 0.479747    
## poly(Olaparib, 3)1:genotypeALC1KO                       -4.812 5.54e-06 ***
## poly(Olaparib, 3)2:genotypeALC1KO                        4.404 2.76e-05 ***
## poly(Olaparib, 3)3:genotypeALC1KO                        0.067 0.946526    
## siRNAsi53BP1:genotypeALC1KO                              2.018 0.046427 *  
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                      0.142 0.887657    
## siRNAsiBRCA1:genotypeALC1KO                              4.032 0.000111 ***
## poly(Olaparib, 3)1:siRNAsi53BP1:genotypeALC1KO           0.690 0.492028    
## poly(Olaparib, 3)2:siRNAsi53BP1:genotypeALC1KO          -1.011 0.314418    
## poly(Olaparib, 3)3:siRNAsi53BP1:genotypeALC1KO           0.351 0.725996    
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO  -0.357 0.721994    
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO  -0.977 0.331069    
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1:genotypeALC1KO  -0.811 0.419389    
## poly(Olaparib, 3)1:siRNAsiBRCA1:genotypeALC1KO           1.240 0.218019    
## poly(Olaparib, 3)2:siRNAsiBRCA1:genotypeALC1KO          -2.329 0.021958 *  
## poly(Olaparib, 3)3:siRNAsiBRCA1:genotypeALC1KO           0.423 0.673509    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 0.09227 on 96 degrees of freedom
## Multiple R-squared:  0.9367, Adjusted R-squared:  0.9162 
## F-statistic: 45.82 on 31 and 96 DF,  p-value: < 2.2e-16
cat("AIC: ", AIC(fit11))
## AIC:  -217.6213
simres <- simulateResiduals(fittedModel = fit11)
plot(simres)

fit12 <- lmer(Counts ~ poly(Olaparib,3)*siRNA*genotype + (1|UID), data = dataset)
print(summary(fit12))
## Linear mixed model fit by REML. t-tests use Satterthwaite's method [
## lmerModLmerTest]
## Formula: Counts ~ poly(Olaparib, 3) * siRNA * genotype + (1 | UID)
##    Data: dataset
## 
## REML criterion at convergence: 1309.1
## 
## Scaled residuals: 
##      Min       1Q   Median       3Q      Max 
## -2.43519 -0.42342  0.02777  0.45257  2.33975 
## 
## Random effects:
##  Groups   Name        Variance Std.Dev.
##  UID      (Intercept) 200467   447.7   
##  Residual              28016   167.4   
## Number of obs: 128, groups:  UID, 32
## 
## Fixed effects:
##                                                        Estimate Std. Error
## (Intercept)                                             2126.62     227.74
## poly(Olaparib, 3)1                                     -4063.13     473.42
## poly(Olaparib, 3)2                                     -1834.91     473.42
## poly(Olaparib, 3)3                                      -658.33     473.42
## siRNAsi53BP1                                             -39.75     322.08
## siRNAsi53BP1+siBRCA1                                    -504.87     322.08
## siRNAsiBRCA1                                           -1185.69     322.08
## genotypeALC1KO                                         -1216.75     322.08
## poly(Olaparib, 3)1:siRNAsi53BP1                         -944.12     669.52
## poly(Olaparib, 3)2:siRNAsi53BP1                          302.40     669.52
## poly(Olaparib, 3)3:siRNAsi53BP1                          486.10     669.52
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1                 1233.64     669.52
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1                 1565.84     669.52
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1                 1284.68     669.52
## poly(Olaparib, 3)1:siRNAsiBRCA1                          199.10     669.52
## poly(Olaparib, 3)2:siRNAsiBRCA1                         2351.59     669.52
## poly(Olaparib, 3)3:siRNAsiBRCA1                          593.91     669.52
## poly(Olaparib, 3)1:genotypeALC1KO                      -2177.12     669.52
## poly(Olaparib, 3)2:genotypeALC1KO                       3444.07     669.52
## poly(Olaparib, 3)3:genotypeALC1KO                        375.79     669.52
## siRNAsi53BP1:genotypeALC1KO                             -182.19     455.49
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                       28.87     455.49
## siRNAsiBRCA1:genotypeALC1KO                              519.06     455.49
## poly(Olaparib, 3)1:siRNAsi53BP1:genotypeALC1KO          2942.95     946.85
## poly(Olaparib, 3)2:siRNAsi53BP1:genotypeALC1KO         -1295.71     946.85
## poly(Olaparib, 3)3:siRNAsi53BP1:genotypeALC1KO            77.89     946.85
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO  1730.08     946.85
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO -2295.16     946.85
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1:genotypeALC1KO -1183.92     946.85
## poly(Olaparib, 3)1:siRNAsiBRCA1:genotypeALC1KO          4018.95     946.85
## poly(Olaparib, 3)2:siRNAsiBRCA1:genotypeALC1KO         -3685.15     946.85
## poly(Olaparib, 3)3:siRNAsiBRCA1:genotypeALC1KO          -196.83     946.85
##                                                              df t value
## (Intercept)                                               24.00   9.338
## poly(Olaparib, 3)1                                        72.00  -8.582
## poly(Olaparib, 3)2                                        72.00  -3.876
## poly(Olaparib, 3)3                                        72.00  -1.391
## siRNAsi53BP1                                              24.00  -0.123
## siRNAsi53BP1+siBRCA1                                      24.00  -1.568
## siRNAsiBRCA1                                              24.00  -3.681
## genotypeALC1KO                                            24.00  -3.778
## poly(Olaparib, 3)1:siRNAsi53BP1                           72.00  -1.410
## poly(Olaparib, 3)2:siRNAsi53BP1                           72.00   0.452
## poly(Olaparib, 3)3:siRNAsi53BP1                           72.00   0.726
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1                   72.00   1.843
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1                   72.00   2.339
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1                   72.00   1.919
## poly(Olaparib, 3)1:siRNAsiBRCA1                           72.00   0.297
## poly(Olaparib, 3)2:siRNAsiBRCA1                           72.00   3.512
## poly(Olaparib, 3)3:siRNAsiBRCA1                           72.00   0.887
## poly(Olaparib, 3)1:genotypeALC1KO                         72.00  -3.252
## poly(Olaparib, 3)2:genotypeALC1KO                         72.00   5.144
## poly(Olaparib, 3)3:genotypeALC1KO                         72.00   0.561
## siRNAsi53BP1:genotypeALC1KO                               24.00  -0.400
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                       24.00   0.063
## siRNAsiBRCA1:genotypeALC1KO                               24.00   1.140
## poly(Olaparib, 3)1:siRNAsi53BP1:genotypeALC1KO            72.00   3.108
## poly(Olaparib, 3)2:siRNAsi53BP1:genotypeALC1KO            72.00  -1.368
## poly(Olaparib, 3)3:siRNAsi53BP1:genotypeALC1KO            72.00   0.082
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO    72.00   1.827
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO    72.00  -2.424
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1:genotypeALC1KO    72.00  -1.250
## poly(Olaparib, 3)1:siRNAsiBRCA1:genotypeALC1KO            72.00   4.245
## poly(Olaparib, 3)2:siRNAsiBRCA1:genotypeALC1KO            72.00  -3.892
## poly(Olaparib, 3)3:siRNAsiBRCA1:genotypeALC1KO            72.00  -0.208
##                                                        Pr(>|t|)    
## (Intercept)                                            1.84e-09 ***
## poly(Olaparib, 3)1                                     1.25e-12 ***
## poly(Olaparib, 3)2                                     0.000232 ***
## poly(Olaparib, 3)3                                     0.168641    
## siRNAsi53BP1                                           0.902805    
## siRNAsi53BP1+siBRCA1                                   0.130079    
## siRNAsiBRCA1                                           0.001174 ** 
## genotypeALC1KO                                         0.000922 ***
## poly(Olaparib, 3)1:siRNAsi53BP1                        0.162804    
## poly(Olaparib, 3)2:siRNAsi53BP1                        0.652870    
## poly(Olaparib, 3)3:siRNAsi53BP1                        0.470172    
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1                0.069508 .  
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1                0.022128 *  
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1                0.058975 .  
## poly(Olaparib, 3)1:siRNAsiBRCA1                        0.767041    
## poly(Olaparib, 3)2:siRNAsiBRCA1                        0.000771 ***
## poly(Olaparib, 3)3:siRNAsiBRCA1                        0.377997    
## poly(Olaparib, 3)1:genotypeALC1KO                      0.001747 ** 
## poly(Olaparib, 3)2:genotypeALC1KO                      2.23e-06 ***
## poly(Olaparib, 3)3:genotypeALC1KO                      0.576353    
## siRNAsi53BP1:genotypeALC1KO                            0.692708    
## siRNAsi53BP1+siBRCA1:genotypeALC1KO                    0.949978    
## siRNAsiBRCA1:genotypeALC1KO                            0.265711    
## poly(Olaparib, 3)1:siRNAsi53BP1:genotypeALC1KO         0.002695 ** 
## poly(Olaparib, 3)2:siRNAsi53BP1:genotypeALC1KO         0.175428    
## poly(Olaparib, 3)3:siRNAsi53BP1:genotypeALC1KO         0.934667    
## poly(Olaparib, 3)1:siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.071813 .  
## poly(Olaparib, 3)2:siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.017864 *  
## poly(Olaparib, 3)3:siRNAsi53BP1+siBRCA1:genotypeALC1KO 0.215209    
## poly(Olaparib, 3)1:siRNAsiBRCA1:genotypeALC1KO         6.43e-05 ***
## poly(Olaparib, 3)2:siRNAsiBRCA1:genotypeALC1KO         0.000220 ***
## poly(Olaparib, 3)3:siRNAsiBRCA1:genotypeALC1KO         0.835913    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
cat("AIC: ", AIC(fit12))
## AIC:  1377.126
simres <- simulateResiduals(fittedModel = fit12)
plot(simres)

Compare Results

ICtab(fit1,fit2,fit3,fit4,
      fit5,fit6,fit7,fit8,
      fit9,fit10,fit11,fit12,
      base=T)
##       AIC    dAIC   df
## fit7  -228.2    0.0 25
## fit11 -217.6   10.5 33
## fit3  -192.1   36.1 17
## fit6   -73.3  154.9 25
## fit10  -62.8  165.4 33
## fit2   -31.3  196.8 17
## fit12 1377.1 1605.3 34
## fit8  1479.1 1707.2 26
## fit4  1658.4 1886.5 18
## fit1  1889.3 2117.4 20
## fit5  1893.5 2121.7 28
## fit9  1908.2 2136.4 36

Final Result

fit <- fit7

output <- coef(summary(fit))
output <- output[grep("Olaparib", rownames(output)),]

rownames(output) <- gsub("poly\\(|, [1-3]\\)","", rownames(output) )
rownames(output) <- gsub("genotype",  paste0(" ",levels(dataset$genotype)[1], " vs. "), rownames(output))
rownames(output)[!(grepl("vs", rownames(output)))] <- paste(rownames(output)[!(grepl("vs", rownames(output)))], levels(dataset$genotype)[1],  sep = " in " )

rownames(output) <- gsub("siRNA",  paste0(" ",levels(dataset$siRNA)[1], " vs. "), rownames(output))
rownames(output)[!(grepl("vs.*vs|in", rownames(output)))] <- paste(rownames(output)[!(grepl("vs.*vs|in", rownames(output)))], levels(dataset$siRNA)[1],  sep = " in " )

rownames(output)[!(grepl("vs", rownames(output)))] <- paste(rownames(output)[!(grepl("vs", rownames(output)))], levels(dataset$siRNA)[1],  sep = " " )

# suggested result table
kable(output, row.names = T)
Estimate Std. Error t value Pr(>|t|)
Olaparib1 in WT siCtrl -1.6591091 0.2561505 -6.4770871 0.0000000
Olaparib2 in WT siCtrl -0.7408465 0.2561505 -2.8922312 0.0046590
Olaparib1: siCtrl vs. si53BP1 in WT -0.3425124 0.3622515 -0.9455099 0.3465902
Olaparib2: siCtrl vs. si53BP1 in WT 0.1439674 0.3622515 0.3974238 0.6918695
Olaparib1: siCtrl vs. si53BP1+siBRCA1 in WT -0.0200466 0.3622515 -0.0553389 0.9559746
Olaparib2: siCtrl vs. si53BP1+siBRCA1 in WT 0.7351549 0.3622515 2.0294045 0.0449712
Olaparib1: siCtrl vs. siBRCA1 in WT -1.0827417 0.3622515 -2.9889225 0.0034938
Olaparib2: siCtrl vs. siBRCA1 in WT 0.8309079 0.3622515 2.2937320 0.0238166
Olaparib1: WT vs. ALC1KO in siCtrl -1.7762418 0.3622515 -4.9033385 0.0000035
Olaparib2: WT vs. ALC1KO in siCtrl 1.6254326 0.3622515 4.4870277 0.0000187
Olaparib1: siCtrl vs. si53BP1: WT vs. ALC1KO 0.3600258 0.5123010 0.7027623 0.4837740
Olaparib2: siCtrl vs. si53BP1: WT vs. ALC1KO -0.5278751 0.5123010 -1.0304002 0.3052125
Olaparib1: siCtrl vs. si53BP1+siBRCA1: WT vs. ALC1KO -0.1862640 0.5123010 -0.3635831 0.7169074
Olaparib2: siCtrl vs. si53BP1+siBRCA1: WT vs. ALC1KO -0.5099282 0.5123010 -0.9953684 0.3218674
Olaparib1: siCtrl vs. siBRCA1: WT vs. ALC1KO 0.6472261 0.5123010 1.2633708 0.2092808
Olaparib2: siCtrl vs. siBRCA1: WT vs. ALC1KO -1.2156753 0.5123010 -2.3729707 0.0194828
write.table(output, file = "Figure5A_Stats_Ref_WT.txt", quote = F, sep = "\t", row.names = T, col.names = NA)
# re-fit with ALC1KO reference
dataset$genotype <- relevel(dataset$genotype, ref = "ALC1KO")
 
fit <- lm(NormCounts2 ~ poly(Olaparib,2)*siRNA*genotype, data = dataset)

output <- coef(summary(fit))
output <- output[grep("Olaparib", rownames(output)),]

rownames(output) <- gsub("poly\\(|, [1-3]\\)","", rownames(output) )
rownames(output) <- gsub("genotype",  paste0(" ",levels(dataset$genotype)[1], " vs. "), rownames(output))
rownames(output)[!(grepl("vs", rownames(output)))] <- paste(rownames(output)[!(grepl("vs", rownames(output)))], levels(dataset$genotype)[1],  sep = " in " )

rownames(output) <- gsub("siRNA",  paste0(" ",levels(dataset$siRNA)[1], " vs. "), rownames(output))
rownames(output)[!(grepl("vs.*vs|in", rownames(output)))] <- paste(rownames(output)[!(grepl("vs.*vs|in", rownames(output)))], levels(dataset$siRNA)[1],  sep = " in " )

rownames(output)[!(grepl("vs", rownames(output)))] <- paste(rownames(output)[!(grepl("vs", rownames(output)))], levels(dataset$siRNA)[1],  sep = " " )


# suggested result table
kable(output, row.names = T)
Estimate Std. Error t value Pr(>|t|)
Olaparib1 in ALC1KO siCtrl -3.4353509 0.2561505 -13.4114549 0.0000000
Olaparib2 in ALC1KO siCtrl 0.8845861 0.2561505 3.4533843 0.0008020
Olaparib1: siCtrl vs. si53BP1 in ALC1KO 0.0175134 0.3622515 0.0483460 0.9615332
Olaparib2: siCtrl vs. si53BP1 in ALC1KO -0.3839077 0.3622515 -1.0597822 0.2916988
Olaparib1: siCtrl vs. si53BP1+siBRCA1 in ALC1KO -0.2063106 0.3622515 -0.5695231 0.5702293
Olaparib2: siCtrl vs. si53BP1+siBRCA1 in ALC1KO 0.2252266 0.3622515 0.6217411 0.5354727
Olaparib1: siCtrl vs. siBRCA1 in ALC1KO -0.4355156 0.3622515 -1.2022465 0.2319983
Olaparib2: siCtrl vs. siBRCA1 in ALC1KO -0.3847674 0.3622515 -1.0621553 0.2906254
Olaparib1: ALC1KO vs. WT in siCtrl 1.7762418 0.3622515 4.9033385 0.0000035
Olaparib2: ALC1KO vs. WT in siCtrl -1.6254326 0.3622515 -4.4870277 0.0000187
Olaparib1: siCtrl vs. si53BP1: ALC1KO vs. WT -0.3600258 0.5123010 -0.7027623 0.4837740
Olaparib2: siCtrl vs. si53BP1: ALC1KO vs. WT 0.5278751 0.5123010 1.0304002 0.3052125
Olaparib1: siCtrl vs. si53BP1+siBRCA1: ALC1KO vs. WT 0.1862640 0.5123010 0.3635831 0.7169074
Olaparib2: siCtrl vs. si53BP1+siBRCA1: ALC1KO vs. WT 0.5099282 0.5123010 0.9953684 0.3218674
Olaparib1: siCtrl vs. siBRCA1: ALC1KO vs. WT -0.6472261 0.5123010 -1.2633708 0.2092808
Olaparib2: siCtrl vs. siBRCA1: ALC1KO vs. WT 1.2156753 0.5123010 2.3729707 0.0194828
write.table(output, file = "Figure5A_Stats_Ref_ALC1.txt", quote = F, sep = "\t", row.names = T, col.names = NA)

Anova

fit7a <- lm(NormCounts2 ~ poly(Olaparib,2)*siRNA*genotype, data = dataset)
fit7b <- lm(NormCounts2 ~ poly(Olaparib,2)*siRNA+genotype, data = dataset)

# anova table
anova(fit7a, fit7b)
## Analysis of Variance Table
## 
## Model 1: NormCounts2 ~ poly(Olaparib, 2) * siRNA * genotype
## Model 2: NormCounts2 ~ poly(Olaparib, 2) * siRNA + genotype
##   Res.Df     RSS  Df Sum of Sq      F  Pr(>F)    
## 1    104 0.85297                                 
## 2    115 2.00791 -11   -1.1549 12.802 5.2e-15 ***
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1